Full coding hepatitis E virus genotype 3 genome amplification method

•A new amplification method for the complete HEV coding genome was described.•HEV genome organization and function were reviewed.•Polymorphic amino acids of each HEV genome region were analyzed in reference sequences.•Complete coding HEV sequence of an immunocompromised patient with acute infection...

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Bibliographic Details
Published in:Journal of virological methods 2016-04, Vol.230, p.18-23
Main Authors: Muñoz-Chimeno, M., Forero, J.E., Echevarría, J.M., Muñoz-Bellido, J.L., Vázquez-López, L., Morago, L., García-Galera, M.C., Avellón, A.
Format: Article
Language:English
Subjects:
Complete genome
Genome, Viral
Genomics - methods
Hepatitis E - virology
Hepatitis E virus
Hepatitis E virus - genetics
HEV
Humans
Immunocompromised
Mutation
Open Reading Frames
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Summary:•A new amplification method for the complete HEV coding genome was described.•HEV genome organization and function were reviewed.•Polymorphic amino acids of each HEV genome region were analyzed in reference sequences.•Complete coding HEV sequence of an immunocompromised patient with acute infection was analyzed. 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).
ISSN:0166-0934
1879-0984
DOI:10.1016/j.jviromet.2016.01.004