title: Ultra-deep sequencing analysis of the hepatitis A virus 5'-untranslated region among cases of the same outbreak from a single source.
abstract: Hepatitis A virus (HAV) is a causative agent of acute viral hepatitis for which an effective vaccine has been developed. Here we describe ultra-deep pyrosequences (UDPSs) of HAV 5'-untranslated region (5'UTR) among cases of the same outbreak, which arose from a single source, associated with a revolving sushi bar. We determined the reference sequence from HAV-derived clone from an attendant by the Sanger method. Sixteen UDPSs from this outbreak and one from another sporadic case were compared with this reference. Nucleotide errors yielded a UDPS error rate of < 1%. This study confirmed that nucleotide substitutions of this region are transition mutations in outbreak cases, that insertion was observed only in non-severe cases, and that these nucleotide substitutions were different from those of the sporadic case. Analysis of UDPSs detected low-prevalence HAV variations in 5'UTR, but no specific mutations associated with severity in these outbreak cases. To our surprise, HAV strains in this outbreak conserved HAV IRES sequence even if we performed analysis of UDPSs. UDPS analysis of HAV 5'UTR gave us no association between the disease severity of hepatitis A and HAV 5'UTR substitutions. It might be more interesting to perform ultra-deep sequencing of full length HAV genome in order to reveal possible unknown genomic determinants associated with disease severity. Further studies will be needed.
authors.affiliation: 1. Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Shuang
authors.initials: S
authors.lastname: Wu
authors.affiliation: 2. Department of Molecular Virology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Nakamoto
authors.affiliation: 1. Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Kanda
authors.affiliation: 1. Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Xia
authors.initials: X
authors.lastname: Jiang
authors.affiliation: 1. Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: 1. Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Miyamura
authors.affiliation: 2. Department of Molecular Virology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Shirasawa
authors.affiliation: 3. Department of Gastroenterology, National Hospital Organization Chiba Medical Center, 4-1-2 Tsubakimori, Chiba (260-8606), Japan.
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Sugiura
authors.affiliation: 4. Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba (260-8673), Japan.
authors.forename: Azusa
authors.initials: A
authors.lastname: Takahashi-Nakaguchi
authors.affiliation: 4. Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba (260-8673), Japan.
authors.forename: Tohru
authors.initials: T
authors.lastname: Gonoi
authors.affiliation: 1. Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba (260-8677), Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Yokosuka
mesh_terms: D020121:5' Untranslated Regions; D000328:Adult; D004196:Disease Outbreaks; D005260:Female; D006506:Hepatitis A / Q000453:epidemiology* / Q000821:virology*; D030041:Hepatitis A virus / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007564:Japan / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D012270:Ribosomes / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D020121:5' Untranslated Regions
keywords: 5'UTR.; Acute liver failure; HAV; IRES; UDPS