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. 2018 Oct 23;15(1):163.
doi: 10.1186/s12985-018-1082-8.

A new hepatitis E virus genotype 2 strain identified from an outbreak in Nigeria, 2017

Bo Wang  1 , Olusola Anuoluwapo Akanbi  1 , Dominik Harms  1 , Olufisayo Adesina  1 , Folakemi Abiodun Osundare  1   2 , Dhamari Naidoo  3 , Isabel Deveaux  4 , Opeayo Ogundiran  4 , Uzoma Ugochukwu  4 , Nwando Mba  4 , Chikwe Ihekweazu  4 , C-Thomas Bock  5   6
Affiliations

A new hepatitis E virus genotype 2 strain identified from an outbreak in Nigeria, 2017

Bo Wang et al. Virol J. .

Abstract

Background: In 2017 the Nigerian Ministry of Health notified the World Health Organization (WHO) of an outbreak of hepatitis E located in the north-east region of the country with 146 cases with 2 deaths. The analysis of the hepatitis E virus (HEV) genotypes responsible for the outbreak revealed the predominance of HEV genotypes 1 (HEV-1) and 2 (HEV-2). Molecular data of HEV-2 genomes are limited; therefore we characterized a HEV-2 strain of the outbreak in more detail.

Finding: The full-length genome sequence of an HEV-2 strain (NG/17-0500) from the outbreak was amplified using newly designed consensus primers. Comparison with other HEV complete genome sequences, including the only HEV-2 strain (Mex-14) with available complete genome sequences and the availability of data of partial HEV-2 sequences from Sub-Saharan Africa, suggests that NG/17-0500 belongs to HEV subtype 2b (HEV-2b).

Conclusions: We identified a novel HEV-2b strain from Sub-Saharan Africa, which is the second complete HEV-2 sequence to date, whose natural history and epidemiology merit further investigation.

Keywords: Complete genome; HEV genotype 2; HEV subtype 2b; Hepatitis E virus; Nigeria; Outbreak.

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Conflict of interest statement

Ethics approval and consent to participate

Not applicable. German public health institute (RKI) is authorized to receive blood residuals from diagnostics for surveillance purposes (Infection Protection Act IfSG §13). All samples analysed were anonymised.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Phylogenetic relationships of NG/17–0500 within the species Orthohepevirus A. HEV-2 strains are designated with geno/subtype, accession number, country, and collection year. NG/17–0500 of this study is shown in red. Phylogenetic analyses were performed with MEGA software version 7.0.26. Maximum likelihood trees based on General Time Reversible model with Gamma distributed with Invariant sites was inferred. The values at nodes indicate the bootstrap values (using 1000 replications). Values below 70% are hidden for clarity of presentation. Reference sequences for HEV genotypes were as proposed from the ICTV Hepeviridae Study Group. Nucleotide (nt) and amino acid (aa) sequences were aligned using MAFFT software version 7.222. a Phylogenetic relationships based on complete genome sequences of representative HEV reference strains. HEV-2 strains are highlighted with red branches. b Phylogenetic relationships based on 641 nt of ORF 2 corresponding to nt positions 6453 to 7093 (numbered according to the HEV prototype strain from Burma GenBank accession No. M73218). HEV-2b strains are highlighted with red branches
Fig. 2
Fig. 2
Detection of potential recombination events of NG/17–0500 within HEV-1 to HEV-4. a Identity Plot and b BootScan analyses of full-length sequences were performed using SimPlot software program version 3.5.1 with an F84 distance model, a sliding window size of 300 base pairs and a step size of 15 base pairs increment. Positions containing gaps were stripped from the alignment
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