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Identification and comparative analysis of hepatitis B virus genotype D/E recombinants in Africa

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Abstract

Globally, there are approximately 240 million people chronically infected with hepatitis B virus (HBV)—a major cause of hepatocellular carcinoma. Ten different HBV genotypes (A–J) have been identified with distinct geographic distributions. Novel variants generated by recombination between different HBV genotypes have been documented worldwide and represent an important element of genetic variability with possible clinical implications. Here, the complete genome sequence of an HBV genotype D/E recombinant from Ghana is reported. The full-length sequence was obtained using rolling circle amplification followed by PCR and sequenced using next-generation sequencing (NGS). A consensus sequence was extracted from the NGS data and underwent phylogenetic analysis to determine genotype, as well as the recombination pattern. Subsequently, the sequence was compared to recombinants described previously in Africa. Based on MCMC phylogenetic analysis, SimPlot recombination analyses, and intragroup genetic distance, the isolate 007N full-length genome is unique compared to other reported D/E recombinants in Africa.

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Acknowledgements

The initial study was funded by a 2012 International Developmental Grant from the Lifespan/Tufts/Brown CFAR (P30AI042853) and the Brown/Tufts AIDS International Training and Research Program (D43TW000237) to Drs. Archampong and Kwara. Additional support was provided by Brown University—University of Ghana partnership through a USAID/HED Grant (Award# AEG-A-00-05-00007). Dr. Kwara received additional support from Fogarty international Center (D43TW010055). HBV amplicon-seq was conducted by Genomics, Epigenomics and Sequencing Core at the Department of Environmental Health, University of Cincinnati, which was supported in part through CEG Grant (NIEHS P30-ES006096).

Author information

Author notes

  1. Awewura Kwara

    Present address: Division of Infectious Diseases and Global Medicine, University of Florida, Gainesville, FL, USA

Authors and Affiliations

  1. Division of Digestive Disease, University of Cincinnati College of Medicine, Cincinnati, OH, USA

    Ceejay L. Boyce & Jason T. Blackard

  2. Division of Viral Hepatitis, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA

    Lilia Ganova-Raeva

  3. Department of Medicine and Therapeutics, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana

    Timothy N. A. Archampong, Margaret Lartey & Adjoa Obo-Akwa

  4. Korle-Bu Teaching Hospital, Accra, Ghana

    Timothy N. A. Archampong, Margaret Lartey & Ernest Kenu

  5. Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana

    Kwamena W. Sagoe

  6. School of Public Health, College of Health Sciences, University of Ghana, Accra, Ghana

    Ernest Kenu

  7. Warren Alpert Medical School of Brown University, Providence, RI, USA

    Awewura Kwara

  8. The Miriam Hospital, Providence, RI, USA

    Awewura Kwara

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  1. Ceejay L. Boyce
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  2. Lilia Ganova-Raeva
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Correspondence to Jason T. Blackard.

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The authors declare that they have no conflict of interest.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. For this type of case study, formal consent is not required.

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Edited by Wolfram Gerlich.

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Boyce, C.L., Ganova-Raeva, L., Archampong, T.N.A. et al. Identification and comparative analysis of hepatitis B virus genotype D/E recombinants in Africa. Virus Genes 53, 538–547 (2017). https://doi.org/10.1007/s11262-017-1469-4

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  • DOI: https://doi.org/10.1007/s11262-017-1469-4

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