Molecular Characterization of Near Full-Length Genomes of Hepatitis B Virus Isolated from Predominantly HIV Infected Individuals in Botswana

Anderson, Motswedi; Choga, Wonderful T.; Moyo, Sikhulile; Bell, Trevor Graham; Mbangiwa, Tshepiso; Phinius, Bonolo B.; Bhebhe, Lynnette; Sebunya, Theresa K.; Lockman, Shahin; Marlink, Richard; Kramvis, Anna; Essex, Max; Musonda, Rosemary; Blackard, Jason T.; Gaseitsiwe, Simani

doi:10.3390/genes9090453

Cited by 19 publications

(36 citation statements)

References 121 publications

(182 reference statements)

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“…With the aid of a phylogenetic tree, we were able to show that HBV in our participants belongs to genotype A and mostly subgenotype A1. Our observation is in accordance with the previous studies that reported genotype A as the most prevalent HBV genotype in Southern Africa . Using an amino acid alignment, we observed protein sequence differences between sequences from participants and the reference genotype A sequence.…”

Section: Discussionsupporting

confidence: 92%

“…Our observation is in accordance with the previous studies that reported genotype A as the most prevalent HBV genotype in Southern Africa. 40,41 Using an amino acid alignment, we observed protein sequence differences between sequences from participants and the reference genotype A the MHR observed in two participants was previously reported. 42 The commonly described sG145R mutation associated with OBI was not found in our study.…”

Section: Discussionmentioning

confidence: 58%

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High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

Msomi

Ndlovu

Giandhari

et al. 2019

Journal of Medical Virology

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Occult hepatitis B virus (HBV) infection (OBI) is defined as the presence of HBV DNA in the liver with or without detectable HBV DNA in the serum of individuals testing HBV surface antigen (HBsAg) negative using currently available assays. The prevalence of OBI among patients receiving hemodialysis (HD) treatment remains poorly characterized in South Africa despite the high prevalence of HBV. We sought to determine the prevalence of OBI in HD units in tertiary hospitals of KwaZulu‐Natal and to characterize the HBV S gene mutations potentially responsible for OBI. A cross‐sectional descriptive study of residual diagnostic plasma samples from 85 HBsAg‐negative patients receiving HD treatment was included. The PreS/S gene was amplified with a nested HBV polymerase chain reaction for downstream next‐generation sequencing, to determine the viral genotype and identify S gene mutations associated with OBI. Nine of the 85 samples had OBI, based on detectable HBV DNA. The point prevalence of OBI was 10.6% (95% control interval: 5.5%‐19.1%). Phylogenetic analysis of the samples with OBI showed that all belonged to genotype A. Three (~33%) samples had mutations in the major hydrophilic region (MHR) within the S gene, three (~33%) had mutations within the S gene but outside the MHR, whilst the remaining three had no mutations observed. The prevalence of OBI in HBsAg‐negative patients undergoing HD was 10.6%, suggesting that OBI is a clinically significant problem in patients with HD in this region. The screening methods for HBV infection need to be revised to include nucleic acid testing.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 58%

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

Msomi

Ndlovu

Giandhari

et al. 2019

Journal of Medical Virology

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“…The algorithm developed above was used to determine the impact of 43 OBI-associated mutations from Botswana, which have been described in detail elsewhere [ 73 ]. Several of these mutations have been characterized in vitro previously, while others have been reported but not functionally characterized in vitro.…”

Section: Resultsmentioning

confidence: 99%

“…The sequencing of the HBV genomes was reported in detail elsewhere [ 73 ]. Briefly, nearly whole HBV genome was successfully sequenced from 50 of 109 participants (37 CHB and 72 OBI positive) using big dye sequencing chemistry.…”

Section: Methodsmentioning

confidence: 99%

“…Briefly, nearly whole HBV genome was successfully sequenced from 50 of 109 participants (37 CHB and 72 OBI positive) using big dye sequencing chemistry. The nearly whole genome fragment (3 kb excluding the precore region) was amplified by nested PCR [ 73 ]. Online databases were used to determine the genotypes; Geno2pheno available at and Stanford HBV database available at .…”

Section: Methodsmentioning

confidence: 99%

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In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm

Anderson

Choga

Moyo

et al. 2018

Genes

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Occult hepatitis B infections (OBI) represent a reservoir of undiagnosed and untreated hepatitis B virus (HBV), hence the need to identify mutations that lead to this phenotype. Functionally characterizing these mutations by in vitro studies is time-consuming and expensive. To bridge this gap, in silico approaches, which predict the effect of amino acid (aa) variants on HBV protein function, are necessary. We developed an algorithm for determining the relevance of OBI-associated mutations using in silico approaches. A 3 kb fragment of subgenotypes A1 and D3 from 24 chronic HBV-infected (CHB) and 24 OBI participants was analyzed. To develop and validate the algorithm, the effects of 68 previously characterized occult-associated mutations were determined using three computational tools: PolyPhen2, SNAP2, and PROVEAN. The percentage of deleterious mutations (with impact on protein function) predicted were 52 (76.5%) by PolyPhen2, 55 (80.9%) by SNAP2, and 65 (95.6%) by PROVEAN. At least two tools correctly predicted 59 (86.8%) mutations as deleterious. To identify OBI-associated mutations exclusive to Botswana, study sequences were compared to CHB sequences from GenBank. Of the 43 OBI-associated mutations identified, 26 (60.5%) were predicted by at least two tools to have an impact on protein function. To our knowledge, this is the first study to use in silico approaches to determine the impact of OBI-associated mutations, thereby identifying potential candidates for functional analysis to facilitate mechanistic studies of the OBI phenotype.

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In silico functional and structural characterization of hepatitis B virus PreS/S-gene in Iranian patients infected with chronic hepatitis B virus genotype D

Khodadad

Seyedian

Moattari

et al. 2020

Heliyon

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Objective: Chronic hepatitis B (CHB) virus infection is the most prevalent chronic liver disease and has become a serious threat to human health. In this study, we attempted to specify and predict several properties including physicochemical, mutation sites, B-cell epitopes, phosphorylation sites, N-link, O-link glycosylation sites, and protein structures of S protein isolated from Ahvaz. Materials and methods: Initially, hepatitis B virus DNA (HBV DNA) was extracted from five sera samples of untreated chronic hepatitis B patients. The full-length HBV genomes were amplified and then cloned in pTZ57 R/T vector. The full sequences of HBV were registered in the GenBank with accessions numbers (MK355500), (MK355501) and (MK693107-9). PROTSCALE, Expasy's ProtParam, immuneepitope, ABCpred, BcePred, Bepipred, Algpred, VaxiJen, SCRATCH, DiANNA, plus a number of online analytical processing tools were used to analyse and predict the preS/S gene of genotype D sequences. The present study is the first analytical research on samples obtained from Ahvaz. Results: We found major hydrophilic region (MHR) mutations at "a" determining region that included K122R, N131T, F134Y, P142L, and T126N mutations. Moreover, Ahvaz sequences revealed four sites (4, 112, 166, and 309) in the preS/S gene for N-glycosylation that could possibly be a potential target for anti-HBV therapy. Conclusion: In the present study, mutations were identified at positions T113S and N131T within the MHR region of S protein; these mutations can potentially decrease the effect of hepatitis B vaccination in vaccine recipients.

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Molecular Characterization of Near Full-Length Genomes of Hepatitis B Virus Isolated from Predominantly HIV Infected Individuals in Botswana

Cited by 19 publications

References 121 publications

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu‐Natal, South Africa

In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm

In silico functional and structural characterization of hepatitis B virus PreS/S-gene in Iranian patients infected with chronic hepatitis B virus genotype D

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