Full coding hepatitis E virus genotype 3 genome amplification method

Journal of Virological Methods
M Muñoz-ChimenoA Avellón

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 helica...Continue Reading

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Citations

Jun 26, 2018·Reviews in Medical Virology·Florence NicotJacques Izopet
Jul 27, 2018·Transboundary and Emerging Diseases·Ignacio García-BocanegraAntonio Rivero-Juarez
Jan 21, 2019·Journal of Viral Hepatitis·Antonio Rivero-JuarezAntonio Rivero
May 30, 2020·The Journal of General Virology·Donald B SmithMichael A Purdy
May 18, 2019·Journal of Viral Hepatitis·Sebastien LhommeJacques Izopet
May 28, 2019·Transboundary and Emerging Diseases·J Caballero-GómezA Rivero-Juarez
Sep 19, 2020·Microorganisms·Milagros Muñoz-ChimenoAna Avellon
Feb 13, 2020·Frontiers in Microbiology·Nerea GarcíaDavid Rodríguez-Lázaro
Feb 16, 2021·Frontiers in Microbiology·Florence NicotJacques Izopet
Sep 20, 2019·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Jacques IzopetSébastien Lhomme

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Datasets Mentioned

BETA
KU513561
EU723516
EU723515

Methods Mentioned

BETA
PCR
electrophoresis
deubiquitination

Software Mentioned

MegaAlign
Seqman
Mega

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