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Analysis of hepatitis B virus-mixed genotype infection by ultra deep pyrosequencing in Sudanese patients, 2015–2016

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Abstract

Purpose

The frequency of detection of HBV co-infection with multiple HBV genotypes is influenced by the detection method; usually co-infections are detected by multiplex PCR or hybridization assays, and are rarely confirmed by sequencing and conventional cloning. The objective of this study was to confirm by ultra-deep pyrosequencing (UDPS) mixed HBV infections, previously detected by multiplex-nested PCR.

Methods

Sixteen samples from HBV co-infected Sudanese patients detected by multiplex-nested PCR, were amplified targeting the P/S region and sequenced by UDPS.

Results

The only genotypes identified using UDPS were D and E, while A, B, C and F genotypes, previously detected by multiplex-nested PCR, were not detected. Specifically, 10 samples were shown to be mono-infected (D or E); in 3 out of 10 mono-infected D patients, a subtype combination was observed: D1 + D7 in 2 cases and D2 + D6 in 1 case. The remaining 6 subjects were D + E co-infected (harboring different mixtures of D subtypes).

Conclusions

Overall, UDPS is more effective than multiplex-nested PCR for identifying multiple HBV genotypes and subtypes infections.

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Acknowledgements

This work was supported by Italian Ministry of Health (funds Ricerca Corrente, linea 3 hepatitis to National Institute for Infectious Diseases INMI IRCCS L. Spallanzani); the European Union’s Horizon 2020 research and innovation program European Virus Archive goes Global under Grant agreement no. 653316.

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Author notes

  1. Khalid Abdallah Enan and Claudia Minosse contributed equally to this work.

Authors and Affiliations

  1. Department of Virology, Central Laboratory, The Ministry of Higher Education and Scientific Research, 7099, Khartoum, Sudan

    Khalid Abdallah Enan, Abdel Rahim Mohammed El Hussein, Mohamed Omer Mustafa & Dina Ahamed Hassan

  2. Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani”-IRCCS, Via Portuense, 292, 00149, Rome, Italy

    Claudia Minosse, Marina Selleri, Emanuela Giombini, Maria Rosaria Capobianchi & Anna Rosa Garbuglia

  3. Department of Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, 7099, Khartoum, Sudan

    Isam Mohamed Elkhidir & Osama Mohamed Khair

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  1. Khalid Abdallah Enan
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Correspondence to Anna Rosa Garbuglia.

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Enan, K.A., Minosse, C., El Hussein, A.R.M. et al. Analysis of hepatitis B virus-mixed genotype infection by ultra deep pyrosequencing in Sudanese patients, 2015–2016. Infection 47, 793–803 (2019). https://doi.org/10.1007/s15010-019-01306-5

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  • DOI: https://doi.org/10.1007/s15010-019-01306-5

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