Genotyping & diagnostic methods for hepatitis C virus: A need of low-resource countries

A Study on the Prevalence of HCV Genotypes and the Effect of Direct-Acting Antiviral Therapy on Clinical and Laboratory Parameters in HCV-Infected Patients at a Tertiary Care Center in North India

Background

The purpose of this study was to investigate the prevalence and distribution of different HCV genotypes, as well as to evaluate clinical and laboratory parameters in HCV-infected patients before and after DAA treatment.

Material and Methods

An open-label prospective study was conducted on 50 HCV-infected individuals. The HCV-infected patients underwent a baseline evaluation with complete history, examination, and other clinical investigations. These patients received the appropriate DAA according to the genotype for 3 months. At the end of 3 months, these patients were again evaluated clinically.

Results

The majority of instances were among younger age groups. Genotype 3 (66%) was the most common. There was a statistically significant difference found in clinical parameters regarding total bilirubin (p=0.008), SGOT (p=0.001), SGPT (p=0.035), ALP (p=<0.001) and Blood Urea Nitrogen (p = 0.004). When 1a vs 1b intragroup comparison was drawn, there was a significant mean difference found in SGOT (p value= 0.053) and Creatinine (p=0.050) parameters while rest shows no significant difference when associated. In the comparison of 1a vs 3 or 4, none of the parameters shows significant difference while; when 1b vs 3 or 4 comparison was laid out, SGOT and Creatinine was found near to significant.

Conclusion

This study concludes that with the availability of DAAs, highly effective, short-duration, and safe regimens have created better outcomes for patients with HCV infection, especially in those groups where SVR was low with prior therapies or in those where IFN-based treatment strategies were contraindicated.

Promising Schiff bases in antiviral drug design and discovery

Emerging and re-emerging illnesses will probably present a new hazard of infectious diseases and have fostered the urge to research new antiviral agents. Most of the antiviral agents are analogs of nucleosides and only a few are non-nucleoside antiviral agents. There is quite a less percentage of marketed/clinically approved non-nucleoside antiviral medications. Schiff bases are organic compounds that possess a well-demonstrated profile against cancer, viruses, fungus, and bacteria, as well as in the management of diabetes, chemotherapy-resistant cases, and malarial infections. Schiff bases resemble aldehydes or ketones with an imine/azomethine group instead of a carbonyl ring. Schiff bases have a broad application profile not only in therapeutics/medicine but also in industrial applications. Researchers have synthesized and screened various Schiff base analogs for their antiviral potential. Some of the important heterocyclic compounds like istatin, thiosemicarbazide, quinazoline, quinoyl acetohydrazide, etc. have been used to derive novel Schiff base analogs. Keeping in view the outbreak of viral pandemics and epidemics, this manuscript compiles a review of Schiff base analogs concerning their antiviral properties and structural-activity relationship analysis.

Circulating miRNA-192 and miR-29a as Disease Progression Biomarkers in Hepatitis C Patients with a Prevalence of HCV Genotype 3

MicroRNAs miR-29a and miR-192 are involved in inflammatory and fibrotic processes of chronic liver disease, and circulating miR-29a is suggested to diagnose fibrosis progression due to hepatitis C virus (HCV) infection. This study aimed to evaluate the expression profile of circulating miR-192 and 29a in a patient cohort with a high frequency of HCV genotype-3. A total of 222 HCV blood samples were collected and serum were separated. Patients were classified into mild, moderate, and severe liver injury based on their Child-Turcotte-Pugh CTP score. RNA was isolated from the serum and used for quantitative real-time PCR. The HCV genotype-3 (62%) was the predominant HCV genotype. In HCV patients, the serum miR-192 and miR-29a levels were significantly upregulated in comparison to healthy controls (p = 0.0017 and p = 0.0001, respectively). The progression rate of miR-192 and 29a in the patient group with mild was highly upregulated compared to patients with moderate and severe hepatitis infection. The ROC curve of miR-192 and miR-29a of moderate liver disease had a significant diagnostic performance compared to the other HCV-infected groups. The increase in miR-29a and miR-192 serum levels was even slightly higher in patients with HCV genotype-3 than in non-genotype-3 patients. In conclusion, serum miR-192 and miR-29a levels significantly increased during the progression of chronic HCV infection. The marked upregulation in patients with HCV genotype-3 suggests them as potential biomarkers for hepatic disease, independently of the HCV genotype.

Hepatitis C Virus Exposure and Infection in the Perinatal Period

BACKGROUND

Hepatitis C virus infection is a leading cause of blood-borne hepatitis disease worldwide. Hepatitis C is a silent liver disease that, without treatment, leads to late-onset complications, including chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma, in 10-40% of patients.

OBJECTIVE

This study aimed to review the epidemiology, clinical features, diagnosis, treatment, and prevention of hepatitis C among perinatally exposed children.

METHODS

Public databases, including MEDLINE and PubMed, and websites from the Centers for Disease Control and Prevention, the Food and Drug Administration, the World Health Organization, and the National Institutes of Health were searched for relevant articles published between 2006 and 2021.

RESULTS

The prevalence of hepatitis C has increased among women of childbearing age in the United States and is associated with risk factors, such as intravenous drug use, health inequities, and low socioeconomic background. Infants born to hepatitis C virus-infected mothers have a 6% risk of vertical transmission, and among those infected, 75% will develop chronic hepatitis C and late complications. However, hepatitis C-exposed infants are frequently lost to follow-up, and those infected have delayed diagnosis and treatment and are at high risk for late-onset complications. Direct- acting antivirals and the establishment of effective treatment guidelines cure hepatitis C virus infections.

CONCLUSION

Hepatitis C predominantly affects underserved communities. Early screening of mothers and infants is critical for the diagnosis, treatment, and prevention of chronic infections and lateonset complications. New policies are needed to address hepatitis C health care inequities affecting mothers and infants in the United States.

First report on molecular docking analysis and drug resistance substitutions to approved HCV NS5A and NS5B inhibitors amongst Iranian patients

Background

NS5A and NS5B proteins of hepatitis C virus (HCV) are the main targets of compounds that directly inhibit HCV infections. However, the emergence of resistance-associated substitutions (RASs) may cause substantial reductions in susceptibility to inhibitors.

Methods

Viral load and genotyping were determined in eighty-seven naïve HCV-infected patients, and the amplified NS5A and NS5B regions were sequenced by Sanger sequencing. In addition, physicochemical properties, structural features, immune epitopes, and inhibitors-protein interactions of sequences were analyzed using several bioinformatics tools.

Results

Several amino acid residue changes were found in NS5A and NS5B proteins; however, we did not find any mutations related to resistance to the treatment in NS5B. Different phosphorylation and few glycosylation sites were assessed. Disulfide bonds were identified in both proteins that had a significant effect on the function and structure of HCV proteins. Applying reliable software to predict B-cell epitopes, 3 and 5 regions were found for NS5A and NS5B, respectively, representing a considerable potential to induce the humoral immune system. Docking analysis determined amino acids involved in the interaction of inhibitors and mentioned proteins may not decrease the drug efficiency.

Conclusions

Strong interactions between inhibitors, NS5A and NS5B proteins and the lack of efficient drug resistance mutations in the analyzed sequences may confirm the remarkable ability of NS5A and NS5B inhibitors to control HCV infection amongst Iranian patients. The results of bioinformatics analysis could unveil all features of both proteins, which can be beneficial for further investigations on HCV drug resistance and designing novel vaccines.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12876-021-01988-y.

Genotyping simplified: rationally designed antisense oligonucleotide-mediated PCR amplification-free colorimetric sensing of viral RNA in HCV genotypes 1 and 3

Molecular diagnosis of viral genotyping devoid of polymerase chain reaction (PCR) amplification in clinical cohorts has hitherto been challenging. Here we present a simplified molecular diagnostic strategy for direct genotyping of hepatitis C virus (HCV) 1 and 3 (prevalent worldwide) using a combination of rationally designed genotype-specific antisense oligonucleotides (ASOs) and plasmonic gold nanoparticles. The ASOs specific to genotypes 1 and 3 have been designed from the nonstructural region 5A (NS5A) of the viral genome using the ClustalW multiple sequence alignment tool. A total of 79 clinical samples including 18 HCV genotype 1, 18 HCV genotype 3, one HIV positive, one HBV positive, and 41 healthy controls have been tested against both the designed ASOs. The study reveals 100% specificity and sensitivity with the employed samples and thereby opens up new avenues for PCR-free direct genotyping of other viruses as well, through the rational design of ASOs.

HCV virology and diagnosis

Hepatitis C virus (HCV) infection is a major cause of severe liver disease including chronic hepatitis, cirrhosis and hepatocellular carcinoma. The HCV burden in public health is estimated at about 71 million people worldwide by World Health Organization (WHO) with at least 400,000 people that died every year from HCV disease [1]. New hepatitis C treatments with oral direct-acting antivirals (DAAs) showing high rates of response, with short treatment duration [2] have been available. HCV can now be eradicated with minimal side effects. Unfortunately, there is no vaccine yet available, but the development of a safe prophylactic vaccine remains a medical priority [3]. For this purpose, Hepatitis B-C subviral envelope particles can be produced by industrialized procedure. It seems to be very promising as this HBV-HCV vaccine candidate has been shown to elicit a broadly cross neutralizing activity against HCV [4]. Despite this revolution in the HCV-treatment, one of major challenge to achieve a global eradication of HCV remains to reduce the under diagnosis. The low rate of diagnosis is a major obstacle in resources limited countries and is mainly due to the cost of molecular tools, that are essential to diagnose and follow chronic HCV infection. In another hand, the mild clinical symptoms observed in HCV chronic disease, may explain that the majority of HCV infected individuals are unaware of their infection, because HCV testing is not generalized, like it is for HIV. HCV was discovered in 1989 after many years of work, by several researchers, who recently obtained the Nobel price [5-7]. This major discovery allowed the description of the HCV genome and later on of the virus replication and cell cycle, and also, importantly, the development of diagnostic tests for the detection of HCV antibodies (Ab) and RNA who were a priority in transfusion. In this review, we will try to get into the virology and cell biology of HCV. Thereafter, we will discuss the different categories of laboratory tests to diagnose/explore HCV infected subjects.

Previous history of surgery in females and roadside shaving in males are the commonest risk factors for hepatitis C infection: A cross-sectional retrospective study

Background and objectives

Hepatitis C virus (HCV) is a causative agent of hepatitis C disease of the liver. We have analysed the major risk factors including demographic, clinical and genotypic distribution among HCV seropositive patients and their distribution in Uttar Pradesh, India.

Methods

This study was conducted by a questionnaire-based proforma, filled in Hepatobiliary Clinic, Department of Medicine, King Georg's Medical University, Lucknow, from 2014 to 2017. Demographic, clinical and laboratory data were recorded. Seropositivity was demonstrated through an anti-HCV IgG ELISA kit. Positive patients were further examined for HCV RNA by RT-PCR.

Results

A total of 31,440 patients attended the hepatobiliary clinic. Among these, 310 (0.99%) patients were confirmed for HCV infection and there was no significant difference between males and females (50.3% vs. 49.7%). Previous surgery (49.0%), dental extraction (41.0%) and roadside shaving (38.1%) were the major risk factors for HCV infection. We also observed that previous surgery 143/154 (92.9%) in female and roadside shaving 118/156 (75.6%) in male was the commonest factor for HCV, however; dental extraction was comparable among male and female (65 [51.8%] vs 62 [48.2%], P value = 0.818). HCV RNA genotype 3 (81.6%) was the most frequent followed by 3a (11.3%), 3b (5.8%), 1 (0.7%) and 4 (0.7%). In the district-wise analysis, frequent cases were included from Lucknow with previous surgery and dental extraction as the commonest risk factor.

Interpretation and Conclusions

Previous surgery among female and roadside shaving among males are the commonest risk factors for HCV. This study suggests a powerful and strict guideline, to avoid HCV infection.

Changes of Gut-Microbiota-Liver Axis in Hepatitis C Virus Infection

Simple Summary

Gut microbiota alteration is linked to many health disorders including hepatitis C virus (HCV) infection. This dysbiosis in turn impacts the coordination between the gut and the liver that is known as the gut–liver-axis. Here, we discuss the latest findings regarding the changes in gut microbiota structure and functionality post HCV infection and its treatment regimens. In addition, we underline the contribution of the microbiota alterations to HCV associated liver complications.

Abstract

The gut–liver-axis is a bidirectional coordination between the gut, including microbial residents, the gut microbiota, from one side and the liver on the other side. Any disturbance in this crosstalk may lead to a disease status that impacts the functionality of both the gut and the liver. A major cause of liver disorders is hepatitis C virus (HCV) infection that has been illustrated to be associated with gut microbiota dysbiosis at different stages of the disease progression. This dysbiosis may start a cycle of inflammation and metabolic disturbance that impacts the gut and liver health and contributes to the disease progression. This review discusses the latest literature addressing this interplay between the gut microbiota and the liver in HCV infection from both directions. Additionally, we highlight the contribution of gut microbiota to the metabolism of antivirals used in HCV treatment regimens and the impact of these medications on the microbiota composition. This review sheds light on the potential of the gut microbiota manipulation as an alternative therapeutic approach to control the liver complications post HCV infection.

Molecular Characterization of Hepatitis C Virus for Developed Antiviral Agents Resistance Mutations and New Insights into in-silico Prediction Studies

Background

Identification and characterization of developed antiviral drug resistance mutations are key to the success of antiviral therapies against hepatitis C virus (HCV), which remains a worldwide highly prevalent pathogenic disease. Although most studies focus on HCV genotypes 1, 2 or 3, the investigation of drug resistance in HCV genotype 4, predominant in North Africa, is especially significant in Egypt.

Methods

We performed mutational and genotypic analysis of the untranslated region (UTR) and nonstructural protein 5B (NS5B) drug resistance-associated regions of HCV for patients in the surrounding villages of Mansoura city, who were not responding to different antiviral treatments (sofosbuvir (SOF), ribavirin, and interferon). Furthermore, molecular modelling approaches (homology modelling and docking studies) were used to investigate the significance of the identified NS5B mutations for SOF and ribavirin binding in the HCV genotype 4a NS5B active site.

Results

Genotypic analysis confirmed all samples to have genotype 4 with sub-genotype 4a predominant. Partial sequencing of the UTR and NS5B resistance-associated regions identified D258E, T282S and A307G mutations in all isolates of NS5B. The UTR mutation site at position 243 was associated with interferon resistance, whereas the NS5B T282S mutation was considered as significant for SOF and ribavirin resistance. Docking studies in the HCV genotype 4a homology model predict SOF and ribavirin to accommodate a nucleotide-like binding mode, in which the T282 residue does interfere with the binding as it would in HCV genotypes 1 and 2. Mutation energy calculations predict T282S to moderately destabilize the binding of SOF and ribavirin by 0.57 and 0.47 kcal/mol, respectively.

Conclusion

The performed study identified and characterized several antiviral drug resistance mutations of HCV genotype 4a and proposed a mechanism by which the T282S mutation may contribute to SOF and ribavirin resistance.

Study of the Effect of Different Hepatitis C Virus Genotypes on Splenomegaly

Background

Several recent studies have shown that the hepatitis C virus (HCV) and its different genotypes are a predominant and leading cause of cirrhosis and splenomegaly in different regions of the world. Advanced stage of cirrhosis leads to portal hypertension that causes splenomegaly. This complication may have many other manifestations such as anemia, infections, and bleeding disorders in severe stages. This study aimed to determine the effect of different HCV genotypes on the development of splenomegaly and to assess which HCV genotypes are more associated with it.

Materials and methods

A total of 483 conveniently sampled HCV patients were included in this descriptive cross-sectional study. Six genotypes (1, 2a, 2b, 3a, 3b, and mixed) were studied, and 80 patients for each of these genotypes were included. Data were collected from patient medical records regarding patient demographic details, HCV serology and genotyping, and sonographic size of the spleen.

Results

In total, splenomegaly was present in 14.1% (n=68) patients. The development of splenomegaly was significantly associated with old age, as 25.2% (n=26) of patients above 60 years of age (n=103) developed splenomegaly (P=0.005). Our study determined that splenomegaly was significantly related to HCV genotypes 3a, 3b, and 1 (P<0.001, P=0.017, and P=0.019, respectively). By taking mixed genotype as a reference, the odds of developing splenomegaly with genotype 3a were the highest (OR = 9.481; CI=95%).

Conclusions

Our study concludes that HCV genotype 3a, 3b, and 1, and age above 60 years have a significant association with splenomegaly. Genotype 3a has the highest risk of developing splenomegaly. Therefore, our study demands screening, early diagnosis, and prompt treatment of these particular HCV genotypes to prevent complications and risk of mortality.

Hepatitis C Reinfection in People Who Inject Drugs in Resource-Limited Countries: A Systematic Review and Analysis

Hepatitis C (HCV) is a global pandemic. The World Health Organization has developed a strategic plan for HCV elimination that focuses on low- and middle-income countries (LMICs) and high-risk populations, including people who inject drugs (PWID). While direct-acting antiviral (DAA) therapies are highly effective at eliminating HCV infections and have few side effects, medical professionals and policymakers remain concerned about the risk of reinfection among PWID. This study is a systematic review of research measuring the rate of HCV reinfection among PWID in LMICs and identifies additional areas for further research. A systematic search strategy was used to identify studies documenting HCV reinfection after sustained virologic response in PWID in LMICs. We refined results to include studies where at least 50% of participants had DAA treatment for primary HCV infection. Pooled reinfection rate was calculated across all studies. Seven studies met eligibility criteria. Most studies were conducted in six upper middle-income countries (Mexico, Romania, Russia, Taiwan, Georgi, and Brazil) and one lower middle-income country (Bangladesh) with a total of 7665 participants. No study included information from PWID in low-income countries. Sample sizes ranged from 200 to 3004 individuals, with demographic data missing for most participants. Four studies used deep gene sequencing, and reflex genotyping procedures to differentiate reinfection (infection by a different HCV genotype/subtype) from virologic relapse (infection by the same strain). The follow-up time of people cured from primary chronic HCV infection ranged from 12 weeks to 6.6 years. The pooled reinfection rate of all seven studies was 2.8 (range: 0.02 to 10.5) cases per 100 person-years (PY). In the five studies that differentiated relapse from reinfection, the incidence of reinfection was 1.0 per 100 PY. To date, research on reinfection rates among PWID in LMICs remains limited. Research focused on PWID in low-income countries is particularly needed to inform clinical decision making and evidence-based programs. While rates of reinfection among PWID who complete DAA treatment in upper and lower middle-income countries were similar or lower than rates observed in PWID in high-income countries, the rates were highly variable and factors may influence the accuracy of these measurements. This systematic review identifies several areas for continued research. Policies concerning access to HCV testing and treatment should be comprehensive and not place restrictions on PWID in these settings.

Hepatocellular Carcinoma (HCC) in Egypt: A comprehensive overview

BACKGROUND

Worldwide, hepatocellular carcinoma (HCC) is a universal problem and its epidemiological data showed variation from place to place. Hepatocellular carcinoma (HCC) is the sixth and fourth common cancer in worldwide and Egypt, respectively. Egypt ranks the third and 15^th most populous country in Africa and worldwide, respectively. The aim of this review is to compare the status of HCC in Egypt to that in the worldwide from different issues; risk factors, screening and surveillance, diagnosis and treatment, prevention, as well as research strategy.

MAIN BODY

The risk factors for HCC in Egypt are of great importance to be reported. The risk factor for HCC are either environmental- or host/genetic-related risk factors. In the last years, there is a tangible improvement of both screening and surveillance strategies of HCC in Egypt. The unprecedented national screening campaign launched by the end of 2018 is a mirror image of this improvement. While the improvement of the HCC prevention requires the governmental health administration to implement health policies. Although the diagnosis of Egyptian HCC patients follows the international guidelines but HCC treatment options are limited in terms of cost. In addition, there are limited Egyptian reports about HCC survival and relapse. Both basic and clinical HCC research in Egypt are still limited compared to worldwide.

SHORT CONCLUSION

Deep analysis and understanding of factors affecting HCC burden variation worldwide help in customization of efforts exerted to face HCC in different countries especially large country like Egypt. Overall, the presence of a research strategy to fight HCC in Egyptian patients will help in the optimum allocation of available resources to reduce the numbers of HCC cases and deaths and to improve the quality of life.