Key associations for hepatitis C virus genotypes in the Middle East and North Africa

Hepatitis C risk score as a tool to identify individuals with HCV infection: a demonstration and cross-sectional epidemiological study in Egypt

OBJECTIVES

Hepatitis C virus (HCV) infection poses a global health challenge. By the end of 2021, the WHO estimated that less than a quarter of global HCV infections had been diagnosed. There is a need for a public health tool that can facilitate the identification of people with HCV infection and link them to testing and treatment, and that can be customised for each country.

METHODS

We derived and validated a risk score to identify people with HCV in Egypt and demonstrated its utility. Using data from the 2008 and 2014 Egypt Demographic and Health Surveys, two risk scores were constructed through multivariable logistic regression analysis. A range of diagnostic metrics was then calculated to evaluate the performance of these scores.

RESULTS

The 2008 and 2014 risk scores exhibited similar dependencies on sex, age and type of place of residence. Both risk scores demonstrated high and similar areas under the curve of 0.77 (95% CI: 0.76 to 0.78) and 0.78 (95% CI: 0.77 to 0.80), respectively. For the 2008 risk score, sensitivity was 73.7% (95% CI: 71.5% to 75.9%), specificity was 68.5% (95% CI: 67.5% to 69.4%), positive predictive value (PPV) was 27.8% (95% CI: 26.4% to 29.2%) and negative predictive value (NPV) was 94.1% (95% CI: 93.5% to 94.6%). For the 2014 risk score, sensitivity was 64.0% (95% CI: 61.5% to 66.6%), specificity was 78.2% (95% CI: 77.5% to 78.9%), PPV was 22.2% (95% CI: 20.9% to 23.5%) and NPV was 95.7% (95% CI: 95.4% to 96.1%). Each score was validated by applying it to a different survey database than the one used to derive it.

CONCLUSIONS

Implementation of HCV risk scores is an effective strategy to identify carriers of HCV infection and to link them to testing and treatment at low cost to national programmes.

Fibrosis Stage-specific Incidence of Hepatocellular Cancer After Hepatitis C Cure With Direct-acting Antivirals: A Systematic Review and Meta-analysis

BACKGROUND & AIMS

Hepatitis C virus (HCV) eradication with direct-acting antivirals reduces hepatocellular carcinoma (HCC) risk. Pooled HCC incidence rates by cirrhosis status and fibrosis stage have not been estimated using meta-analysis.

METHODS

We searched PubMed, Web of Science, Embase, and Cochrane Library from January 1, 2014 to December 31, 2020 to identify studies assessing HCC incidence or outcomes by cirrhosis status, in adults with HCV who achieved sustained virologic response (SVR) after direct-acting antivirals. Pooled estimates were obtained using random-effects modeling. Subgroup, sensitivity, and meta-regression analyses were performed to evaluate heterogeneity.

RESULTS

We included 31 studies involving 27,711 patients with cirrhosis (mean follow-up, 2.1 years) and 11 studies involving 32,123 patients without cirrhosis (mean follow-up, 2.6 years). HCC incidence was 2.99/100 person-years (95% confidence interval [CI], 2.52-3.54; I2 = 75%) in patients with cirrhosis, 0.47/100 person-years (95% CI, 0.32-0.70, I2 = 71%) in patients without cirrhosis, and 0.63/100 person-years (95% CI: 0.34-1.20, I2 = 0%) in stage 3 (F3) fibrosis. Among patients with cirrhosis, HCC incidence was highest in studies with <1 year of follow-up (6.17/100 person-years [95% CI, 3.73-10.19]) and progressively lower in studies with longer follow-up (1-2 years: 2.75/100 person-years [95% CI, 2.48-3.06]; 2-3 years: 2.90/100 person-years [95% CI, 1.90-4.44]; ≥3 years: 1.83/100 person-years [95% CI, 0.88-3.80]).

CONCLUSION

Pooled HCC incidence after SVR in patients with cirrhosis was very high (2.99/100 person-years) but may be declining as longer time accrues after SVR. In patients without cirrhosis, including F3 fibrosis, HCC incidence was lower than thresholds associated with cost-effective HCC screening. In patients with F3 fibrosis, the lack of between-study heterogeneity provides strong evidence that HCC screening may not be warranted.

Sub-genotypes of hepatitis C virus in the Middle East and North Africa: Patterns of distribution and temporal changes

Infection with the hepatitis C virus (HCV) remains a considerable public health concern in the Middle East and North Africa (MENA). The objectives of this study were to analyze the HCV genotype (GT) and sub-genotype (SGT) distribution in the MENA region and to assess the temporal change in the number of sequences within the MENA region. All HCV molecular sequences collected in the MENA region had been retrieved from GenBank as of 1 August 2022. The number of HCV sequences retrieved was 6740 representing sequences from a total of 17 MENA countries with a majority from Iran (n = 1969, 29.2%), Egypt (n = 1591, 23.6%), Tunisia (n = 1305, 19.4%) and Saudi Arabia (n = 1085, 16.1%). The determination of GT/SGT was based on the NCBI genotyping and Blast tool. Genotype 1 (GT1) dominated infections in the MENA (n = 2777, 41.2%), followed by GT4 (n = 2566, 39.0%). Additionally, SGT4a (1515/6393, 23.7%) was the most common SGT in the MENA, and SGT4a was dominant in Egypt and Saudi Arabia, followed by SGT1b (n = 1308, 20.5%), which was dominant in Morocco and Tunisia, while SGT1a (n = 1275, 19.9%) was common in Iran, Iraq and Palestine. Furthermore, significant temporal increase in the number of HCV MENA sequences was observed. On the SGT level, specific patterns of HCV genetic diversity were seen in the MENA region, with the most common SGT being 4a, in addition to increasing the availability of HCV sequences in the MENA region.

Identifying Different Mutation Sites Leading to Resistance to the Direct-Acting Antiviral (DAA) Sofosbuvir in Hepatitis C Virus Patients from Egypt

The hepatitis C virus (HCV) is a major global health challenge and a leading cause of morbidity and mortality. Many direct-acting antivirals (DAAs) target essential macromolecules involved in the virus’ life cycle. Although such DAAs achieve great success in reducing the viral load in genotype 1 infections, other genotypes demonstrate different levels of response. This study focused on mutation sites associated with patients with genotype 4a infections that failed to respond to treatment with sofosbuvir. The genotyping of HCV samples from patients with virological failure, and responder patients, was conducted using Geno2Pheno webserver-based full NS5B sequences. We constructed 3D structural models for all the samples and used structural analysis to investigate the effect of amino acid substitution on the observed resistance to SOF-based treatment, and the docking of sofosbuvir into the active sites of the 10 models was performed. Finally, 10 molecular dynamic (MD) simulation experiments were conducted to compare the stability of the 3D models of the resistant samples against the stability of the 3D models of the responder samples. The results highlighted the presence of HCV subtype 4a in all ten samples; in addition, an amino acid (aa) substitution in the palm region may hinder HCV polymerase activity. In this study, we provide evidence that a mutation in the NS5B gene that induces resistance to sofosbuvir in patients with the S282T/C/R mutant virus is present in the Egyptian population. Overall, the docking and MD results support our findings and highlight the significant impact of the identified mutations on the resistance of HCV NS5B RNA-dependent RNA polymerase to direct-acting antivirals (DAAs).

Hepatitis C virus among blood donors and general population in Middle East and North Africa: Meta-analyses and meta-regressions

BACKGROUND

Despite the Middle East and North Africa (MENA) Region reported to have the highest prevalence of hepatitis C virus (HCV) globally, HCV infection levels in the majority of MENA countries remain inadequately characterized. Blood donor data have been previously used as a proxy to assess levels and trends of HCV in the general population, however, it is unclear how comparable these populations are in MENA and whether blood donors provide an appropriate proxy.

AIM

To delineate HCV epidemiology among blood donors and the general population in the MENA.

METHODS

The data source was the systematically gathered MENA HCV Epidemiology Synthesis Project Database. Random-effects meta-analyses and meta-regressions were conducted. For comparison, analyses were conducted for Europe, utilizing the Hepatitis C Prevalence Database of the European Centre for Disease Prevention and Control.

RESULTS

One thousand two hundred and thirteen HCV antibody prevalence measures and 84 viremic rate measures were analyzed for MENA. Three hundred and seventy-seven antibody prevalence measures were analyzed for Europe. In MENA, pooled mean prevalence was 1.58% [95% confidence interval (CI): 1.48%–1.69%] among blood donors and 4.49% (95%CI: 4.10%–4.90%) in the general population. In Europe, pooled prevalence was 0.11% (95%CI: 0.10%–0.13%) among blood donors and 1.59% (95%CI: 1.25%–1.97%) in the general population. Prevalence in the general population was 1.72-fold (95%CI: 1.50–1.97) higher than that in blood donors in MENA, but it was 15.10-fold (95%CI: 11.48–19.86) higher in Europe. Prevalence was declining at a rate of 4% per year in both MENA and Europe [adjusted risk ratio: 0.96 (95%CI: 0.95–0.97) in MENA and 0.96 (95%CI: 0.92–0.99) in Europe]. Pooled mean viremic rate in MENA was 76.29% (95%CI: 67.64%–84.02%) among blood donors and 65.73% (95%CI: 61.03%–70.29%) in the general population.

CONCLUSION

Blood donor data provide a useful proxy for HCV infection in the wider population in MENA, but not Europe, and could improve HCV burden estimations and assess progress toward HCV elimination by 2030.

Simultaneous Hepatitis C Virus Genotyping and Variant Detection in Patients with Thalassemia: A Single-Center Phylogenetic Study

BACKGROUND: Hepatitis C virus (HCV) genotype distribution is different in various regions. A variety of strategies could be used to detect HCV genotypes and subtypes. The aim of the present study was to introduce a genotyping method by an in-house protocol that could be used to determine HCV drug-resistant variants and phylogeny studies. METHODS: Samples from 91 patients with thalassemia were used for HCV genotyping by Cobas 4800 platform, and 50 cases of 1a, 1b, and 3a genotypes underwent amplification and sequencing of NS5A and NS5B by using consensus primers via conventional reverse transcription-polymerase chain reaction (RT-PCR) method. An ABI 3730xl system used for direct sequencing. Raw sequences were analyzed by popular bioinformatics software MEGA6 and CLC workbench 5. Phylogenetic construction was drawn using 1000 replicates bootstrap by the neighbor-joining method. Multiple sequence alignment (MSA) was performed for mutation detection. RESULTS: Sequencing results of 50 HCV isolates subtypes 1a (31/45), 3a (15/22) and 1b (4/8) NS5A and NS5B genes showed there were 72 NS5A and 105 NS5B mutations. Moreover, 8 resistant associated substitutions (RASs) were identified in nine thalassemia cases by multiple sequence alignment (MSA) protein analysis. The phylogenetic tree construct drew confirmed by the Cobas HCV genotyping results. CONCLUSION: The phylogenetic analysis could be a useful tool for HCV genotyping in case of determining the drug-resistant substitutions; however, it is time-consuming and needs expert analysis and interpretation. This preliminary study in Iranian patients with thalassemia introduces specific conventional RT-PCR to find RASs to direct acting antivirals (DAAs) and subtype determination at the same time.

Impact of Drug Use Policy on the Appropriate Use of Direct Acting Antiviral Agents for Hepatitis C in Saudi Arabia

Background:

Ministry of National Guard–Health Affairs in Saudi Arabia developed a new policy for the use of direct antiviral agents (DAAs) for hepatitis C. The present study was conducted to evaluate prescribers' compliance and the impact of the policy on DAAs appropriate use.

Materials and Methods:

This study was conducted at King Abdul Aziz Medical City in Jeddah, Saudi Arabia. The study compares patients' data during 1 year before and 1 year after policy initiation. The primary outcomes were compliance to monitoring parameters, appropriateness of treatment and treatment eligibility. Secondary outcomes included sustained virologic response at 12 weeks, documentation of potential drug–drug interactions and treatment costs. Independent samples t-test and Chi-square test were used when applicable. A P < 0.05 was considered statistically significant.

Results:

One hundred and three patients were included in analysis (46 before and 57 after policy). Prescriber compliance to baseline monitoring parameters was 67.4% before policy and 82.5% after-policy (P = 0.076). International normalized ratio (INR) was requested in 84.8% of cases before policy compared to 96.5% after-policy (P = 0.036). Treatment options offered to patients were appropriate in 52.2% of cases before policy and in 82.5% after-policy (P = 0.001).

Conclusion:

There is a significant improvement in the baseline monitoring of INR. Treatment options offered after policy implementation were significantly more appropriate.

Characterizing the historical role of parenteral antischistosomal therapy in hepatitis C virus transmission in Egypt

Background

Egypt is the nation most affected by hepatitis C virus (HCV) infection, following an epidemic of historic proportions. We aimed to characterize the epidemic’s historical evolution and to delineate the role of parenteral antischistosomal therapy (PAT) campaigns in transmission.

Methods

A mathematical model was constructed and analysed in order to understand HCV-transmission dynamics. The model was fitted to Egypt’s Demographic and Health Survey data and to a systematic database of HCV-prevalence data.

Results

The incidence rate peaked in 1966 at 15.7 infections per 1000 person-years—a period of time that coincides with the PAT campaigns—and rapidly declined thereafter, beginning the mid-1990s. The annual number of new infections peaked in 1993 at 581 200 (with rapid demographic growth), leading to a high-incidence-cohort effect, and declined to 67 800 by 2018. The number of individuals ever infected (1950–2018) was 16.4 million, with HCV prevalence peaking in 1979. The number of individuals ever exposed to PAT was 8.3 million; however, of these individuals, 7.3 million were alive in 1980 and only 3.5 million alive in 2018. The number of individuals ever infected due to PAT exposure was 963 900, with 850 200 individuals alive in 1980 and only 389 800 alive in 2018. The proportion of PAT-attributed prevalent infections peaked at 19.9% in 1972, declining to 5.5% by 2018.

Conclusions

PAT campaigns played an important role in HCV transmission, yet explain only 6% of infections—they appear to be a manifestation, rather than a cause, of the epidemic. A possible driver of the epidemic could be the mass expansion of inadequate-quality healthcare during PAT campaigns and subsequent decades. Despite a historic toll, the epidemic has been rapidly diminishing since the mid-1990s.

Hepatitis C virus genotypes in patients with chronic hepatitis C infection in southern Iran from 2016 to 2019

Hepatitis C is a liver disease caused by the hepatitis C virus (HCV). The treatment of HCV infection has become more complicated due to various genotypes and subtypes of HCV. The treatment of HCV has made significant advances with direct-acting antivirals. However, for the choice of medicine or the combination of drugs for hepatitis C, it is imperative to detect and discriminate the crucial HCV genotypes. The main objective of this study was to determine the pattern of circulating HCV genotypes in southern Iran, from 2016 until 2019. The other aim of the study was to determine possible associations of patients' risk factors with HCV genotypes. A total of 803 serum samples were collected in 4 years (2016-2019) from patients with HCV antibody positive results. A total of 728 serum samples were HCV-RNA positive. The prevalence of HCV genotypes was detected using the genotype-specific RT-PCR test for serum samples obtained from 615 patients. The HCV genotype 1 (G1) was the most prevalent (48.8%) genotype in the area, with G1a, G1b, and mixed G1a/b representing 38.4%, 10.1%, and 0.3%, respectively. Genotype 3a was the next most prevalent (47.2%). Mixed genotypes 1a/3a were detected in 22 (3.6%) and finally G4 was found in 3 (0.5%) patients. The other HCV genotypes were not detected in any patient. Genotype 1 (1a and 1b alone, 1a/1b and 1a/3a coinfections) is the most prevalent HCV genotype in southern Iran. HCV G1 shows a significantly higher rate in people under 40 years old.

Key associations for hepatitis C virus genotypes in the Middle East and North Africa

This study aimed to investigate the epidemiology of hepatitis C virus (HCV) genotypes in the Middle East and North Africa (MENA) through an analytical and quantitative meta-regression methodology. For the most common genotypes 1, 3, and 4, country/subregion explained more than 77% of the variation in the distribution of each genotype. Genotype 1 was common across MENA, and was more present in high-risk clinical populations than in the general population. Genotype 3 was much more present in Afghanistan, Iran, and Pakistan than the rest of countries, and was associated with transmission through injecting drug use. Genotype 4 was broadly disseminated in Egypt in all populations, with overall limited presence elsewhere. While genotype 2 was more present in high-risk clinical populations and people who inject drugs, most of the variation in its distribution remained unexplained. Genotypes 5, 6, and 7 had low or no presence in MENA, limiting the epidemiological inferences that could be drawn. To sum up, geography is the principal determinant of HCV genotype distribution. Genotype 1 is associated with transmission through high-risk clinical procedures, while genotype 3 is associated with injecting drug use. These findings demonstrate the power of such analytical approach, which if extended to other regions and globally, can yield relevant epidemiological inferences.

Hepatitis C Virus Infection in Populations With Liver-Related Diseases in the Middle East and North Africa

We investigated hepatitis C virus (HCV) epidemiology in populations with liver‐related diseases (LRDs) in the Middle East and North Africa. The data source was standardized databases of HCV measures populated through systematic reviews. Random‐effects meta‐analyses and meta‐regressions were performed, and genotype diversity was assessed. Analyses were based on 252 HCV antibody prevalence measures, eight viremic rate measures, and 30 genotype measures on 132,358 subjects. Pooled mean prevalence in LRD populations was 58.8% (95% confidence interval [CI], 51.5%‐66.0%) in Egypt and 55.8% (95% CI, 49.1%‐62.4%) in Pakistan; these values were higher than in other countries, which had a pooled prevalence of only 15.6% (95% CI, 12.4%‐19.0%). Mean prevalence was highest in patients with hepatocellular carcinoma at 56.9% (95% CI, 50.2%‐63.5%) and those with cirrhosis at 50.4% (95% CI, 40.8%‐60.0%). Type of LRD population and country were the strongest predictors of prevalence, explaining 48.6% of the variation. No evidence for prevalence decline was found, but there was strong evidence for prevalence increase in Pakistan. A strong, positive association was identified between prevalence in the general population and that in LRD populations; the Pearson correlation coefficient ranged between 0.605 and 0.862. The pooled mean viremic rate was 75.5% (95% CI, 61.0%‐87.6%). Genotype 4 was most common (44.2%), followed by genotype 3 (34.5%), genotype 1 (17.0%), genotype 2 (3.5%), genotype 6 (0.5%), and genotype 5 (0.3%). Conclusion: HCV appears to play a dominant role in liver diseases in Egypt and Pakistan and has a growing role in Pakistan. Testing and treatment of LRD populations are essential to reduce disease burden and transmission and to reach HCV elimination by 2030.