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. 2019 Oct;47(5):793-803.
doi: 10.1007/s15010-019-01306-5. Epub 2019 Apr 8.

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

Khalid Abdallah Enan #  1 , Claudia Minosse #  2 , Abdel Rahim Mohammed El Hussein  1 , Marina Selleri  2 , Emanuela Giombini  2 , Maria Rosaria Capobianchi  2 , Isam Mohamed Elkhidir  3 , Mohamed Omer Mustafa  1 , Osama Mohamed Khair  3 , Dina Ahamed Hassan  1 , Anna Rosa Garbuglia  4
Affiliations

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

Khalid Abdallah Enan et al. Infection. 2019 Oct.

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.

Keywords: Co-infection; Hepatitis B virus; High-throughput nucleotide sequencing; Sudan.

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