Phylogenetic analysis of two new complete genomes of the hepatitis E virus (HEV) genotype 3 from Thailand
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ORIGINAL ARTICLE
Phylogenetic analysis of two new complete genomes of the hepatitis E virus (HEV) genotype 3 from Thailand Tipsuda Chanmanee1 · Pravech Ajawatanawong2 · Suda Louisirirotchanakul1 · Watcharasak Chotiyaputta3 · Siwaporn Chainuvati3 · Patimaporn Wongprompitak4 Received: 11 November 2019 / Accepted: 8 October 2020 © The Author(s) 2020
Abstract Hepatitis E virus (HEV) is a causative agent of acute viral hepatitis globally. Evolutionary phylogeny classifies the HEV into eight genotypes that correlate with the viral transmission. Only four genotypes have been proven to be responsible for transmission in humans. However, there has been no report on the genomics and genotyping of HEV in Thailand during the past ten years. Here, we identified the genotype distributions of the Thai isolates of HEV and we sequenced two HEV genomes. We screened for 18 Thai isolates of HEV from Siriraj Hospital in Bangkok, from 2014–2016. The HEV genomes were sequenced from the serum and feces of a patient. The results showed that all Thai isolates of HEV were identified as genotype 3 (HEV-3). The ORF2 and genome phylogenies suggested two subgenotypes, called 3.1 and 3.2. The Thai isolates of HEV were frequently found in the subgenotype 3.1. The genome sequences of the two Thai isolates of HEV from the serum and fecal samples of the same patient showed 91% nucleotide similarity with the HEV genotype 3. Comparisons between the HEV genome and the ORF2 phylogenies illustrated that the ORF2 tree can be used to identify HEV genotypes, but it has less phylogenetic power for the HEV evolution. The two new genome sequences of HEV-3 from Thailand could contribute valuable information to the HEV genome study. (226 words) Keywords Hepatitis E virus · HEV genotype · HEV genotype 3 · Complete genome sequence · Phylogeny
Introduction Hepatitis E virus (HEV) or Orthohepevirus A is an emerging viral infection that causes acute hepatitis, which is considered as leading to a low rate of mortality and not developing into chronic hepatitis [1]. However, the incidence of chronic Tipsuda Chanmanee and Pravech Ajawatanawong are co-first author and also contributed equally to this work. * Patimaporn Wongprompitak [email protected] 1
Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
2
Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
3
Division of Gastroenterology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
4
Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
hepatitis appears to be increasing among immunocompromised patients who have had an organ transplant, in developing countries, particularly industrial countries [2, 3]. The virus transmits when people consume contaminated food or water [1]. There are two main laboratory-detection methods for HEV. One is the molecular-ba
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