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The complete genomes of subgenotype IA hepatitis A virus strains from four different islands in Indonesia form a phylogenetic cluster

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Abstract

Despite the high endemicity of hepatitis A virus (HAV) in Indonesia, genetic information on those HAV strains is limited. Serum samples obtained from 76 individuals during outbreaks of hepatitis A in Jember (East Java) in 2006 and Tangerang (West Java) in 2007 and those from 82 patients with acute hepatitis in Solo (Central Java), Denpasar on Bali Island, Mataram on Lombok Island, and Makassar on Sulawesi Island in 2003 or 2007 were tested for the presence of HAV RNA by reverse transcription PCR with primers targeting the VP1-2B region (481 nucleotides, primer sequences at both ends excluded). Overall, 34 serum samples had detectable HAV RNA, including at least one viremic sample from each of the six regions. These 34 strains were 96.3-100 % identical to each other and formed a phylogenetic cluster within genotype IA. Six representative HAV isolates from each region shared 98.3-98.9 % identity over the entire genome and constituted a IA sublineage with a bootstrap value of 100 %, consisting of only Indonesian strains. HAV strains recovered from Japanese patients who were presumed to have contracted HAV infection while visiting Indonesia were closest to the Indonesian IA HAV strains obtained in the present study, with a high identity of 99.5-99.7 %, supporting the Indonesian origin of the imported strains. These results indicate that genetic analysis of HAV strains indigenous to HAV-endemic countries, including Indonesia, are useful for tracing infectious sources in imported cases of acute hepatitis A and for defining the epidemiological features of HAV infection in that country.

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Acknowledgements

This work was supported in part by a grant from the Ministry of Health, Labour and Welfare of Japan. We are grateful to the Center of Environmental Health and Disease Control of Jakarta and Surabaya for preparing the serum samples from Tangerang and Jember.

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Authors and Affiliations

  1. Immunobiology Laboratory, Faculty of Medicine, University of Mataram, Mataram, Indonesia

    Mulyanto

  2. West Nusa Tenggara Hepatitis Laboratory, Mataram, Indonesia

    Mulyanto

  3. Gastroentero-hepatology Division, Department of Internal Medicine, School of Medicine, Udayana University, Denpasar, Bali, Indonesia

    I Dewa Nyoman Wibawa

  4. Sanglah General Hospital, Denpasar, Bali, Indonesia

    I Dewa Nyoman Wibawa

  5. Department of Clinical Pathology, Moewardi Hospital, University of Sebelas Maret, Solo, Indonesia

    Joseph Benedictus Suparyatmo

  6. Department of Internal Medicine, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia

    Rifai Amirudin

  7. Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan

    Hiroshi Ohnishi, Masaharu Takahashi, Tsutomu Nishizawa & Hiroaki Okamoto

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  1. Mulyanto
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  8. Hiroaki Okamoto
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Corresponding author

Correspondence to Hiroaki Okamoto.

Additional information

Deceased: R. Amirudin.

The nucleotide sequences of HAV isolates reported herein have been assigned DDBJ/EMBL/GenBank accession nos. AB839692-AB839697 (complete genomes) and AB839698-AB839731 (481-nt VP1-2B sequences).

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Mulyanto, Wibawa, I.D.N., Suparyatmo, J.B. et al. The complete genomes of subgenotype IA hepatitis A virus strains from four different islands in Indonesia form a phylogenetic cluster. Arch Virol 159, 935–945 (2014). https://doi.org/10.1007/s00705-013-1874-5

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  • DOI: https://doi.org/10.1007/s00705-013-1874-5

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