title: Full coding hepatitis E virus genotype 3 genome amplification method.
abstract: Hepatitis E virus (HEV) genotype 3 produces zoonotic infection associated with the consumption of infected animals. HEV infections can become chronic in immunocompromised (IC) patients. The viral genome has three well defined open reading frames (ORF1, ORF2 and ORF3) within which various domains and functions have been described. This paper (i) describes a new method of complete sequencing of the HEV coding region through overlapping PCR systems, (ii) establishes a consensus sequence and polymorphic positions (PP) for each domain, and (iii) analyzes the complete coding sequence of an IC patient. With regard to the consensus, a high percentage of PP was observed in protease (PP=19%) and the X domain (PP=22%) within ORF1, the N-terminal region of the S domain (PP=22%) in ORF2, and the P1 (PP=35%) and P2 (PP=25%) domains in ORF3. In contrast, the ORF1 Y, ORF2 S, ORF2 M and ORF3 D1 domains were conserved in the reference sequences (0.40, 1, 0.70 and 0% of PP, respectively). The sequence from the IC patient had more mutations in the RpRp (D1235G, Q1242R, S1454T, V1480I, I1502 V, K1511R, G1373 V, E1442D, V1693 M), the terminal ORF2 S- domain (F10L, S26T, G36S, S70P, A105 V, I113 V), the X domain (T938 M, T856 V, S898A) and the helicase (S1014N, S975T, Q1133 K).
authors.affiliation: Hepatitis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid Spain. Electronic address: milagrosmch@hotmail.com.
authors.forename: M
authors.initials: M
authors.lastname: Muñoz-Chimeno
authors.affiliation: Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Medellín Colombia. Electronic address: jforeroduarte@gmail.com.
authors.forename: J E
authors.initials: JE
authors.lastname: Forero
authors.affiliation: Hepatitis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid Spain. Electronic address: jmecheva@isciii.es.
authors.forename: J M
authors.initials: JM
authors.lastname: Echevarría
authors.affiliation: Microbiology Unit, Salamanca University Hospital, Salamanca Spain. Electronic address: jlmubel@usal.es.
authors.forename: J L
authors.initials: JL
authors.lastname: Muñoz-Bellido
authors.affiliation: Hematology Unit, Salamanca University Hospital, Salamanca Spain. Electronic address: lvazlo@usal.es.
authors.forename: L
authors.initials: L
authors.lastname: Vázquez-López
authors.affiliation: Hepatitis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid Spain. Electronic address: lmorago@isciii.es.
authors.forename: L
authors.initials: L
authors.lastname: Morago
authors.affiliation: Hepatitis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid Spain. Electronic address: Mcgarciagalera@gmail.com.
authors.forename: M C
authors.initials: MC
authors.lastname: García-Galera
authors.affiliation: Hepatitis Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid Spain. Electronic address: aavellon@isciii.es.
authors.forename: A
authors.initials: A
authors.lastname: Avellón
mesh_terms: D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D016751:Hepatitis E / Q000821:virology*; D016752:Hepatitis E virus / Q000235:genetics*; D006801:Humans; D009154:Mutation; D016366:Open Reading Frames
keywords: Complete genome; HEV; Hepatitis E virus; Immunocompromised