Molecular epidemiology, phylogenetic analysis and genotype distribution of hepatitis B virus in Saudi Arabia: Predominance of genotype D1

Contemporary and historical human migration patterns shape hepatitis B virus diversity

Infection by hepatitis B virus (HBV) is responsible for approximately 296 million chronic cases of hepatitis B, and roughly 880,000 deaths annually. The global burden of HBV is distributed unevenly, largely owing to the heterogeneous geographic distribution of its subtypes, each of which demonstrates different severity and responsiveness to antiviral therapy. It is therefore crucial to the global public health response to HBV that the spatiotemporal spread of each genotype is well characterized. In this study, we describe a collection of 133 newly sequenced HBV strains from recent African immigrants upon their arrival in Belgium. We incorporate these sequences-all of which we determine to come from genotypes A, D, and E-into a large-scale phylogeographic study with genomes sampled across the globe. We focus on investigating the spatio-temporal processes shaping the evolutionary history of the three genotypes we observe. We incorporate several recently published ancient HBV genomes for genotypes A and D to aid our analysis. We show that different spatio-temporal processes underlie the A, D, and E genotypes with the former two having originated in southeastern Asia, after which they spread across the world. The HBV E genotype is estimated to have originated in Africa, after which it spread to Europe and the Americas. Our results highlight the use of phylogeographic reconstruction as a tool to understand the recent spatiotemporal dynamics of HBV, and highlight the importance of supporting vulnerable populations in accordance with the needs presented by specific HBV genotypes.

The Effectiveness and Safety of Direct-Acting Antivirals in the Treatment of Hepatitis C Virus in Saudi Arabia: A Nationwide Study Based on the Saudi Ministry of Health Surveillance Data From 2017 to 2021

Background and objective While the Kingdom of Saudi Arabia (KSA) has had a hepatitis C virus (HCV) elimination program in place since 2015, there have been limited studies investigating the effectiveness and safety of direct-acting antivirals (DAAS) based on the Ministry of Health (MOH) surveillance data. In light of this, this study was conducted to assess the effectiveness and safety of DAAS (glecaprevir/pibrentasvir, daclatasvir/sofosbuvir, or other combinations) in treating HCV cases in Saudi Arabia as per the MOH data from 2017 to 2021. Methods This was a retrospective cohort study involving recorded HCV cases in the national hepatitis surveillance database of MOH across all regions of KSA from 2017 to 2021. Statistical analyses were performed using IBM SPSS Statistics software (IBM Corp., Armonk, NY). Continuous variables were expressed as mean ± standard deviation (SD), and categorical variables were presented as numbers (percentages). An independent t-test was used for continuous variables, and a Chi-square analysis was used for categorical variables. A confidence interval of 95%, a margin of error of 0.05, a precision of 2%, and a 5% level of significance were employed. Results Regarding demographic characteristics, age was significantly associated with HCV infection (p=0.002). Similarly, nationality had a highly significant association with HCV infection (p=0.004). Regarding clinical characteristics, creatinine levels were significantly associated with HCV infection (p=0.009). As for effectiveness, all participants had a positive polymerase chain reaction (PCR) for HCV at enrolment (n=4806) and were DAAS-naïve. After the completion of the first DAAS course, 99.5% (4781) had negative PCRs 12 weeks post-treatment completion; however, the PCR remained positive for some patients (0.5%, n=25), which became negative after receiving the second DAAS course, resulting in complete cure of HCV infection and a 100% negative PCR among all participants. With regard to safety, no side effects were recorded in the cohort and hence the safety aspect was not analyzed. Conclusion Univariate analysis revealed that nationality (non-Saudi), age, and creatinine levels were significantly associated with HCV infection. However, only nationality showed a significant association with HCV infection following multivariate logistic regression adjustment. We believe that these insights will help guide the creation of clinical guidelines and promote evidence-based decision-making in the management of HCV in Saudi Arabia.

The role of hepatitis B virus genome variations in HBV-related HCC: effects on host signaling pathways

Hepatocellular carcinoma (HCC) is a significant global health issue, with a high prevalence in many regions. There are variations in the etiology of HCC in different regions, but most cases are due to long-term infection with viral hepatitis. Hepatitis B virus (HBV) is responsible for more than 50% of virus-related HCC, which highlights the importance of HBV in pathogenesis of the disease. The development and progression of HBV-related HCC is a complex multistep process that can involve host, viral, and environmental factors. Several studies have suggested that some HBV genome mutations as well as HBV proteins can dysregulate cell signaling pathways involved in the development of HCC. Furthermore, it seems that the pathogenicity, progression of liver diseases, response to treatment and also viral replication are different among HBV mutants. Understanding the relationship between HBV genome variations and host signaling pathway alteration will improve our understanding of the molecular pathogenesis of HBV-related HCC. Furthermore, investigating commonly dysregulated pathways in HBV-related HCC is necessary to discover more specific therapeutic targets and develop more effective strategies for HCC treatment. The objective of this review is to address the role of HBV in the HCC progression and primarily focus on the impacts of HBV genome variations on HCC-related signaling pathways.

Variable Proportions of Phylogenetic Clustering and Low Levels of Antiviral Drug Resistance among the Major HBV Sub-Genotypes in the Middle East and North Africa

Hepatitis B virus (HBV) infection remains a major public health threat in the Middle East and North Africa (MENA). Phylogenetic analysis of HBV can be helpful to study the putative transmission links and patterns of inter-country spread of the virus. The objectives of the current study were to analyze the HBV genotype/sub-genotype (SGT) distribution, reverse transcriptase (RT), and surface (S) gene mutations and to investigate the domestic transmission of HBV in the MENA. All HBV molecular sequences collected in the MENA were retrieved from GenBank as of 30 April 2021. Determination of genotypes/SGT, RT, and S mutations were based on the Geno2pheno (hbv) 2.0 online tool. For the most prevalent HBV SGTs, maximum likelihood phylogenetic analysis was conducted to identify the putative phylogenetic clusters, with approximate Shimodaira-Hasegawa-like likelihood ratio test values ≥ 0.90, and genetic distance cut-off values ≤ 0.025 substitutions/site as implemented in Cluster Picker. The total number of HBV sequences used for genotype/SGT determination was 4352 that represented a total of 20 MENA countries, with a majority from Iran (n = 2103, 48.3%), Saudi Arabia (n = 503, 11.6%), Tunisia (n = 395, 9.1%), and Turkey (n = 267, 6.1%). Genotype D dominated infections in the MENA (86.6%), followed by genotype A (4.1%), with SGT D1 as the most common in 14 MENA countries and SGT D7 dominance in the Maghreb. The highest prevalence of antiviral drug resistance was observed against lamivudine (4.5%) and telbivudine (4.3%). The proportion of domestic phylogenetic clustering was the highest for SGT D7 (61.9%), followed by SGT D2 (28.2%) and genotype E (25.7%). The largest fraction of domestic clusters with evidence of inter-country spread within the MENA was seen in SGT D7 (81.3%). Small networks (containing 3-14 sequences) dominated among domestic phylogenetic clusters. Specific patterns of HBV genetic diversity were seen in the MENA with SGT D1 dominance in the Levant, Iran, and Turkey; SGT D7 dominance in the Maghreb; and extensive diversity in Saudi Arabia and Egypt. A low prevalence of lamivudine, telbivudine, and entecavir drug resistance was observed in the region, with almost an absence of resistance to tenofovir and adefovir. Variable proportions of phylogenetic clustering indicated prominent domestic transmission of SGT D7 (particularly in the Maghreb) and relatively high levels of virus mobility in SGT D1.

Novel hepatitis B virus subgenotype A8 and quasi-subgenotype D12 in African-Belgian chronic carriers

BACKGROUND

Hepatitis B virus (HBV) is a public health threatening virus and is classified into more than eight genotypes and more than forty subgenotypes.

OBJECTIVES

To characterize and propose novel strains assigned as A8 and D12.

METHODS

Four out of 133 HBV complete genome sequences, isolated from Belgian chronic carriers with African origin were phylogenetically analyzed.

RESULTS

Phylogenetic analyses of HBV genotypes A and D strains exhibited separate clusters supported by significant bootstrap values. The two genotype A strains isolated from Congolese patients, and two genotype D strains isolated from Ghanaian carriers clustered separately from the other known subgenotypes A (A1-A6 and quasi-subgenotypes) and subgenotypes D (D1-D11). The mean inter-subgenotypic nucleotide divergence over the full-length genome sequence between the novel strains (A8 and D12) and A1-A7 and D1-D11 subgenotypes was higher than 4%.

CONCLUSIONS

Phylogenetic analysis of the full-length HBV genome sequences revealed a novel subgenotype and quasi-subgenotype based on the nucleotide divergence and identification of novel amino acids motifs in different ORFs. We identified two strains of the novel subgenotype A8 and two strains of the novel quasi-subgenotype D12. Notably, the analysis demonstrated that the subgenotype A8 strains are a basal lineage that diverged before the other African subgenotypes A.