Genotype Research Articles

Genotype 3 is linked to worse liver disease progression in hepatitis C patients even after SVR following DAA therapy

Background and aimsHCV genotype (GT) 3 is associated with rapid liver disease progression. However, the liver disease progression and its risk factors in patients with HCV GT 3 infection after sustained virological response (SVR) following direct-acting antivirals (DAAs) remain unclear. Therefore, we aimed to investigate the liver disease progression of patients with GT 3 after SVR.MethodsThis was a retrospective cohort study of patients with HCV infection who achieved SVR by DAAs. The clinical outcome was overall liver disease progression (OLDP), defined as newly diagnosed compensated liver cirrhosis, decompensated liver cirrhosis, or hepatocellular carcinoma. The incidence of OLDP was evaluated by Kaplan−Meier analysis. Cox regression analysis identified the risk factors for OLDP.ResultsA total of 409 patients (46.9% GT3) were followed for 43.7 (32.9, 58.7) months. The incidence of OLDP was higher in patients with GT 3 (4.63/100PY) than non-GT 3 (0.60/100PY; P < 0.001). According to Cox multivariate analysis, GT 3 was significantly associated with OLDP (HR 6.41, 95% CI 1.82 - 22.56; P=0.004). The predictors of OLDP in patients with GT 3 were HCV recurrence (HR 12.15, 95% CI 3.18 - 46.46; P < 0.001) and FIB-4 > 3.25 (HR 16.40, 95% CI 1.03 - 39.81; P = 0.046) at baseline.ConclusionHCV GT 3-infected patients remain at a higher risk of OLDP even after achieving SVR by DAAs, especially patients with advanced liver fibrosis and at high risk for reinfection or virological late relapse.

Evaluation of a next generation sequencing assay for Hepatitis B antiviral drug resistance on the oxford nanopore system.

Next-generation sequencing (NGS) for Hepatitis B virus (HBV) antiviral resistance (AVR) testing is a highly sensitive diagnostic method, able to detect low-level mutant subpopulations. Our clinical virology laboratory previously transitioned from DNA hybridization (INNO-LiPA) to NGS, initially with the GS Junior System and subsequently the MiSeq. The Oxford Nanopore Technology (ONT) sequencing system was evaluated for HBV resistance testing, with regards to sequencing accuracy and turn-around time. We performed amplicon sequencing of the HBV polymerase gene from patient plasma and external quality assessment (EQA) samples on the MiSeq Reagent Nano Kit v2 and GridION ONT with R10.4.1 flowcells. Mutational analysis and genotyping were performed by DeepChek®Assay-HBV (version 2.0). A total of 49 patient samples and 15 EQA samples were tested on both the MiSeq and ONT. There was high agreement for both patient and EQA samples between the MiSeq and ONT systems, with regards to total drug resistance mutations detected and total patient sample agreement, 68/70 (97 %) and 47/49 (96 %), respectively. The ONT NGS platform provided accurate HBV AVR results, with improved turn-around times. Sequencing error rates at AVR codons were below 1 %.

Association between extracellular matrix protein 1 (ECM1) gene polymorphisms (rs3834087 and rs3754217) and Hepatitis B Virus evolution in an African cohort.

Hepatitis B virus (HBV) is a significant cause of liver disease and cancer worldwide. Understanding the genetic factors influencing HBV evolution is crucial for developing effective prevention and treatment strategies. Host genetic and environmental factors particularly influence the evolution of this infection. Recent studies have implicated the ECM1 gene in HBV pathogenesis, mainly two specific polymorphisms (rs3834087 and rs3754217). In an African cohort, we comprehensively analyzed these ECM1 gene polymorphisms and their association with HBV evolution.In this case-control analysis, 167 samples, consisting of 59 controls and 108 cases, were examined. The cases included 50 patients with Chronic Hepatitis B(CHB), 16 with cirrhosis, and 42 with hepatocellular carcinoma (HCC). Genomic DNA extraction was executed using INVITROGEN and FAVORGEN kits. Genotyping of rs3834087 and rs3754217 polymorphisms in the ECM1 gene was accomplished via real-time PCR on the QuantStudioTM 5 Real-Time instrument, followed by allelic discrimination using TaqMan Genotyper Software. Data was interpreted using SPSS version 20 and Epi info version 7.5.2.0. Odds ratios (OR), confidence intervals (CI), and p-values were derived for risk and significance evaluation.In our study, the heterozygous genotype (GT) of rs3754217 could confer protection to controls against the onset of chronic hepatitis in the event of infection (OR=0.05; CI=0.006-0.46; p=0.002). In addition, carriage of mutated alleles of the two (2) polymorphisms was associated with the course of infection and may influence the appearance of severe forms at certain stages of the disease.Our study is the first to assess the association between polymorphisms (rs3834087 and rs3754217) in the ECM1 gene and the course of HBV infection in Burkina Faso. It showed that combining specific genotypes of the two (2) polymorphisms would be associated with protection against chronic hepatitis.

Treatment of Hepatitis C Virus Infections Among Patients of Ukrainian Origin During the Influx of War Refugees to Poland.

Background: The wave of wartime migration from Ukraine has raised a number of concerns about infectious diseases, the prevalence of which is higher in Ukraine than in host countries, with hepatitis C virus (HCV) infection being one of them. Our analysis aimed to assess the percentage of HCV-infected Ukrainian refugees under care in Polish centers providing antiviral diagnosis and therapy, to evaluate their characteristics and the effectiveness of treatment with direct-acting antiviral drugs (DAAs). Methods: The analysis included patients of Polish and Ukrainian nationality treated for HCV infection between 2022 and 2024 in Polish hepatology centers. Data were collected retrospectively and completed online. Results: In the population of 3911 patients with chronic hepatitis C treated with DAAs in 16 Polish centers in 2022-2024, there were 429 war refugees from Ukraine, accounting for 11% of the total treated. The Ukrainian population was significantly younger (45.7 vs. 51 years, p < 0.001) and had a higher percentage of women (50.3% vs. 45.3%, p = 0.048) compared to Polish patients. Patients of Ukrainian origin had less advanced liver disease and were significantly less likely to have comorbidities and the need for comedications. Coinfection with human immunodeficiency virus was significantly more common in Ukrainians than in Polish patients, 16.1% vs. 5.9% (p < 0.001). The distribution of HCV genotypes (GTs) also differed; although GT1b predominated in both populations, its frequency was significantly higher in the Polish population (62.3% vs. 44.5%, p < 0.001), while the second most common GT3 was significantly more common in Ukrainian patients (30.5% vs. 16.2%, p < 0.001). Conclusions: Documented differences in patient characteristics did not affect the effectiveness of antiviral therapy, which exceeded 97% in both populations, but there was a higher rate of those lost to follow-up among Ukrainian patients.

Prevalence and drug resistance analysis of hepatitis C virus genotypes in Heilongjiang, China.

Hepatitis C still poses a threat to public safety, and there are few reports of hepatitis C virus (HCV) in Heilongjiang Province. Therefore, we aimed to study the epidemiology and resistance-associated substitutions (RASs) of HCV in Heilongjiang and explore the efficacy of treatment. 7019 specimens from Heilongjiang Province were subjected to the genotype identification. The Autoregressive Integrated Moving Average (ARIMA) model was utilized to predict HCV infection trends from 2024 to 2030. The Sanger sequencing was performed on samples of genotype(GT) 1b and 2a to investigate RASs. Phylogenetic analysis was conducted to assess the similarity of local HCV sequences with those from other countries. In addition, we tracked the effect of patients treated with DAAs and the relationship between efficacy and RASs. The predominant HCV subtypes in Heilongjiang were 1b (47.51%) and 2a (43.85%). From 2012 to 2023, the proportions of GT2a, GT3a, GT3b, and GT6a gradually increased. And the prevalence of GT2a will exceed that of GT1b over the next seven years. The proportion of RASs in GT1b and GT2a NS5A region was 73.47% and 15.22%, respectively. And the proportion of RASs in GT1b NS5B region was 100%. Local HCV sequences exhibited phylogenetic relationships with sequences from other countries. The GT1b R30Q and GT2a C92S were correlated with drug efficacy. K107R and P206S, which have not been reported in the literature, were also related to drug efficacy. The epidemiology of HCV genotypes in Heilongjiang is becoming increasingly diverse. HCV GT1b has a large variety and a high proportion of RASs, and patients infected with this genotype of HCV need to be sequenced before treatment.

Effectiveness of sofosbuvir-based treatments for patients with hepatitis C virus genotype 6 infection: a real-world study from East China.

Over the past decade, the proportion of hepatitis C virus (HCV) genotypes (GT) 1 and 2 has decreased in almost all regions of China, while GT 3 and 6 have emerged as new challenges. GT 6 is unique in many respects, like high genetic variability and emerging resistant variants. This study aims to assess the efficacy of sofosbuvir (SOF)-based treatments in patients with GT 6 chronic hepatitis C (CHC). A retrospective analysis was conducted on patients with GT 6 HCV infection, who were diagnosed between July 2018 and May 2023. All patients received a 12-week course of SOF-based treatments. The primary efficacy endpoint was sustained virologic response (SVR), which is defined as having undetectable HCV RNA at 12 weeks after treatment completion (SVR12). The efficacy data for SVR12 were analyzed using both the evaluated population (EP) and per-protocol population (PP). For the PP populations, efficacy data were stratified using Forrester plots. A total of 201 patients were included in the study. In PP population, the end of treatment virological response rate was 99.48% (190/191), the SVR12 rate was 99.31% (143/144), and the SVR24 rate was 100.00% (75/75). Only one patient with genotype 6a experienced a relapse 12 weeks after the completion of treatment, but her HCV RNA was undetectable both at the end of treatment and 24 weeks after the end of treatment. Additionally, the normalization rates of alanine transaminase (ALT) and aspartate aminotransferase (AST) were significantly higher at the end of treatment (EOT) compared to baseline (27.36% vs. 93.03%, 36.32% vs. 95.02%, p < 0.001). Significant improvements were observed in the levels of total bilirubin, ALT, AST, albumin, globulin, albumin/globulin ratio, gamma-glutamyl transferase, alkaline phosphatase, platelet, fibrosis-4 (FIB-4), and aspartate transaminase to platelet ratio index (APRI) between baseline and EOT (p < 0.05). SOF-based treatments achieved high virological and biochemical response rates in patients with HCV GT 6 infection.

Loss to follow-up of patients after antiviral treatment as an additional barrier to HCV elimination

BackgroundEliminating hepatitis C virus (HCV) infections is a goal set by the World Health Organization. This has become possible with the introduction of highly effective and safe direct-acting antivirals (DAA) but limitations remain due to undiagnosed HCV infections and loss of patients from the cascade of care at various stages, including those lost to follow-up (LTFU) before the assessment of the effectiveness of the therapy. The aim of our study was to determine the extent of this loss and to establish the characteristics of patients experiencing it.MethodsPatients with chronic HCV infection from the Polish retrospective multicenter EpiTer-2 database who were treated with DAA therapies between 2015 and 2023 were included in the study.ResultsIn the study population of 18,968 patients, 106 had died by the end of the 12-week post-treatment follow-up period, and 509 patients did not report for evaluation of therapy effectiveness while alive and were considered LTFU. Among patients with available assessment of sustained virological response (SVR), the effectiveness of therapy was 97.5%. A significantly higher percentage of men (p<0.0001) and a lower median age (p=0.0001) were documented in LTFU compared to the group with available SVR assessment. In LTFU patients, comorbidities such as alcohol (p<0.0001) and drug addiction (p=0.0005), depression (p=0.0449) or other mental disorders (p<0.0001), and co-infection with human immunodeficiency virus (HIV) (p<0.0001) were significantly more common as compared to those with SVR assessment. They were also significantly more often infected with genotype (GT) 3, less likely to be treatment-experienced and more likely to discontinue DAA therapy.ConclusionsIn a real-world population of nearly 19,000 HCV-infected patients, we documented a 2.7% loss to follow-up rate. Independent predictors of this phenomenon were male gender, GT3 infection, HIV co-infection, alcohol addiction, mental illnesses, lack of prior antiviral treatment and discontinuation of DAA therapy.

HCV genotype distribution in Istanbul: Adetailed 7 year epidemiological overview andimpact of Covid-19 pandemic.

Hepatitis C virus (HCV) is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinomaworldwide. HCV has 8 genotypes (GT) and 86 subtypes and distribution of GTs varies based on geographical regions, transmission routes and even in cultural groups. The determination of viral genotype is crucial in choosing antiviral treatment, determining the duration of therapy, and monitoring treatment respose. Since 2014, with the usage of direct-acting antiviral agents (DAAs) in the treatment of HCV infections, a cure rate over 95% could be possible. Epidemiological data are important to combat a chronic HCV infections. Due to its geographical location, Turkey is like a bridge connecting Asia and Europe. Istanbul is the biggest and most crowded city of Turkey and has received immigration from many different countries, especially from Syria, in recent years and immigration still goes on. In addition, the COVID-19 pandemic has had devastating effects in our country. In this study, we determined the HCV genotypes in Health Sciences University Ümraniye Training and Research Hospital, in Istanbul between 2016 and 2022. Of the 322 patients analyzed during this 7-year period, HCV GT1b was the most prevalent GT in 65.2%, followed by GT3 in 15.5%, GT1a in 10.6%. Our data serve as a great mirror for HCV epidemiology in Turkey and contribute to global data.

Hepatitis C virus genotypes among population with reported risk factors in Assam, north-east India: Emergence of genotype-8.

Background & objectives Hepatitis C virus (HCV) exhibits extensive genetic diversity in infected hosts. There are few published reports of HCV genotype (GT) distribution from the north-east Indian States lying close to the 'Golden Triangle' known for illicit drug trafficking. Real-time knowledge of HCVGT distribution is important for studies on epidemiologic aspects and virus evolution and for the development of new target-specific, direct-acting antiviral drugs. This study aims to examine the distribution of HCVGTs and their subtypes in different risk groups from Assam, north-east India. Methods It is a hospital-based cross-sectional study. Plasma samples reactive for anti-HCV antibody in enzyme-linked immunosorbent assay (ELISA) were subjected to viral load test and genotyping by real-time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) or characterization of non-structural protein NS5B region by nested PCR. Nucleotide sequences were subjected to phylogenetic analysis. Results The most common HCVGT detected was GT-3 (95.89%), followed by GT-1 (3.42%), GT-6xa (0.34%) and GT-8 (0.34%). The mean age of subjects was 30.24 yr, and males outnumbered females. The most commonly associated risk factor was injecting drug use (IDU) (74.31%), followed by tattooing and/or piercing (33.22%), transfusion of blood/blood products (10.27%), and haemodialysis (9.25%). Co-infection with human immunodeficiency virus (HIV) was found in 17.8 per cent, and with Hepatitis B virus (HBV) in 3.42 per cent of the cases. Interpretation & conclusions The detection of HCVGT-8 makes this the first report from Assam and the second from India as per the authors' knowledge. This may indicate strain's endemic nature in India. The increasing trend of HCV infection among young IDUs and HCV-HIV co-infection indicates the need for enhancing surveillance and intensified prevention efforts among young adults.

Genotype by environment interaction effect and fresh root yield stability of cassava genotypes under contrasting nitrogen regimes

Nitrogen (N) is an important nutrient element needed by cassava for optimum yield and it is a vital component of nucleotides (nucleic acids), enzymes, amino acids (proteins), chlorophyll molecules and hormones, among other essential compounds required for growth and development of cassava. Nitrogen stress is a major cassava production constraint, the study aimed to examine genotype by environment interaction (GEI) effects and fresh root yield stability of 203 diverse cassava clones to identify genotypes with stable performance under low and optimum nitrogen regimes across environments using AMMI and GGE biplot analysis. Experiments were conducted using an augmented block design with three replications for two years in three locations in Nigeria. There were significant differences (p < 0.001) in the genotype’s mean performances as well as significant differences (p < 0.001) in the environment’s mean performances for all the traits measured in both nitrogen regimes. The AMMI analysis of variance showed significant effects (p < 0.001) for genotypes, environments and the interactions for fresh root yield in both nitrogen regimes. The biplot analysis showed that for fresh root yield in the optimum nitrogen regime, the principal component accounted for 81.54% of the G + GE (Genotype plus and Genotype by Environment) variation. The G + GE for fresh root yield in the low nitrogen regime accounted for a total of 71.64% of the variation. Ten genotypes were identified as the best genotypes under the optimum nitrogen regime, while eleven genotypes were the best under the low nitrogen regime. Three genotypes under optimum nitrogen regimes were high-yielding. Still, they were unstable in their fresh root yield performance across the environments and can be recommended as specifically adapted to the environments they performed best. Three other genotypes were high-yielding genotypes under low nitrogen but were highly unstable in their fresh root yield mean performance across the environments. The environments Otobi_YR1, Igbariam_YR2, and Umudike_YR1 were identified as the most discriminatory among the test environments. The environments Umudike_YR2 and Igbariam_YR1 were identified as the most representative of the test environments and can represent a mega-environment. The best 21 genotypes that performed above the grand mean for fresh root yield in both nitrogen regimes can be further evaluated on the farmer’s field for possible advancement.

Distribution of HCV Genotypes in Patients with Chronic Hepatitis C Infection: A Three-Year Single-Center Retrospective Study

Objective: Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus belonging to the genus Hepacivirus in the Flaviviridae family. It has eight known genotypes and 93 subtypes. HCV can be transmitted through various routes, including blood transfusion, surgical procedures, sexual contact, and intravenous drug use, leading to both acute and chronic hepatitis. Genotype (GT) determination and viral load assessment are essential for selecting an appropriate antiviral treatment regimen and duration, and for monitoring treatment efficacy. We aimed to ascertain the genotype distribution over a three-year period. Methods: In this study, patients diagnosed with chronic HCV infection and followed at Afyonkarahisar Health Sciences University Health Practice and Research Hospital between July 1, 2020, and June 30, 2023, were retrospectively evaluated for their age, gender, and HCV genotype data. Results: A total of 91 patients’ HCV genotype data were included in the study. The study revealed that 95.6% of the patients were Turkish citizens, while 4.4% were of foreign nationality. Among the 91 patients, 60 (65.9%) were found to have genotype 1b, 12 (13.2%) had genotype 1a, 10 (11%) had genotype 3, 6 (6.6%) had genotype 4, 2 (2.2%) had genotype 2, and one patient (1.1%) had a co-infection of genotypes 3 and 4. Conclusion: Genotype 1b was dominant in our region. Identifying HCV genotypes is important in guiding the prognosis and treatment of chronic HCV infections and monitoring the epidemiologic changes. This information will be of great value in the health policy that targets HCV and in elimination efforts.

Real-world experience with direct-acting antiviral therapy in HCV-infected patients with cirrhosis and esophageal varices

BackgroundHepatitis C virus (HCV) infection affects 50 million people worldwide with around 242,000 deaths annually, mainly due to complications such as cirrhosis and hepatocellular carcinoma (HCC). Portal hypertension (PH) caused by cirrhosis leads to severe consequences, including esophageal varices (EV). This study aimed to evaluate the effectiveness and safety of direct-acting antiviral (DAA) treatment in patients with and without EV.MethodsThis retrospective analysis involved consecutive HCV-infected adults undergoing DAA therapy at 22 Polish hepatology centers from July 1, 2015, to December 31, 2022. Patients with cirrhosis were categorized based on the presence of EV diagnosed by gastroscopy. Treatment effectiveness was measured by sustained virologic response (SVR), with safety outcomes monitored for 12 weeks post-treatment.ResultsA population of 3393 HCV-infected patients with cirrhosis was divided into groups with (A, n = 976) and without (B, n = 2417) EV. Group A showed a significantly higher prevalence of comorbidities and concomitant medications. Genotype (GT)1b infections predominated in both groups, and GT3 infections were more common in the EV group. Group A exhibited more severe liver disease, and higher rates of decompensation, HCC, and HBV co-infection. SVR was significantly higher in group B (91.5% vs. 96.3%, p < 0.0001). Male gender, GT3, EV presence, and Child-Pugh grade B were identified as independent negative SVR predictors. Group A had a worse safety profile, with notably higher adverse event incidence and mortality.ConclusionsDAA therapies are highly effective and well tolerated in patients with cirrhosis, but EV presence predicts poorer virologic responses.

Single nucleotide polymorphism profiles of canine T-cell and null-cell lymphomas.

The histopathological classification of T-cell lymphoma (TCL) in humans has distinctive mutational genotyping that suggests different lymphomagenesis. A similar concept is assumed to be observed in dogs with different TCL phenotypes. This study aimed to identify the previously reported single-nucleotide polymorphisms (SNPs) in both human beings and dogs in canine TCLs and null-cell lymphomas (NCLs) and to design compatible oligonucleotides from each variant based on the multiplex polymerase chain reaction. Genomic DNA was extracted from 68 tumor specimens (62 TCLs and 6 NCLs) and 5 buffy coat samples from dogs with TCL. Four TCL subtypes and NCL were analyzed in 44 SNPs from 21 genes using the MassARRAY. The greatest incidences of SNPs observed in all TCL subtypes and NCL ware SATB1 c.1259A > C, KIT c.1275A > G, SEL1L c.2040 + 200C > G, and TP53 c.1024C > T, respectively. Some SNP locations were statistically significant associated with NCL, including MYC p.S75F (p = 0.0003), TP53 p.I149N (p = 0.030), PDCD1 p.F37LX (p = 0.012), and POT1 p.R583* (p = 0.012). Each TCL histological subtype and NCL are likely to contain distinctive mutational genetic profiles, which might play a role in lymphoma gene-risk factors and might be useful for selecting therapeutic target drugs for each canine patient.

Highly accurate single-color fluorogenic DNA decoding sequencing for mutational genotyping

We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3’-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.

Diversity of the Morphometric and Biochemical Traits of Allium cepa L. Varieties.

Several Allium cepa L. varieties, representing a versatile set of vegetables widely utilized by consumers, are appreciated for their bioactive properties, including antimicrobial, anticarcinogenic, and antioxidant capacities. The aim of this study is to compare the morphometric characteristics and biochemical profiles of four cultivars of A. cepa, two of them represented by the perennial Sicilian landrace "Cipudda agghiarola" (Allium × proliferum (Moench) Schrader), widely known as the Egyptian walking onion (WO), and by the landrace "Cipudduzza" belonging to the variety known as aggregatum (ON), which were compared with two commercial cultivars of A. cepa var. cepa (onion), Stoccarda (OS) and Rossa Carmen (OR). The experimental trial was conducted in Catania (Sicily), following organic growing practices. The randomized complete block experimental design was adopted with one experimental factor, the genotype (GE) effect. The harvested plants were characterized for their main morphometric parameters, according to the International Plant Genetic Resources (IGPR) descriptors. The biochemical activity was assessed by analyzing the total phenolic content (TPC) and the total flavonoid content (TFC). The antioxidant capacity was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC). The sugar profile (total sugars, sucrose, glucose, fructose, and fructooligosaccharides-FOS) and the volatile compounds by headspace-gas chromatography/mass spectrometry (HS-GC/MS) were also determined. The OR bulb exhibited the highest TPC (16.3 mg GAE/g d.w., p < 0.01) and TFC (8.5 mg QE/g d.w., p < 0.01), with the highest antioxidant capacity measured by the FRAP (27.1 µmol TE/g d.w., p < 0.01) and DPPH assays (46.2 µmol TE/g d.w., p < 0.01). The ON bulb showed the highest ORAC value (209 µmol TE/g d.w., p < 0.01). Generally, the bulbs were richer in sugars (584 mg/g d.w., p < 0.01) than the leaf blade (239 mg/g d.w., p < 0.01), except for OR. Significant interaction between the genotype and plant organ was noted in the volatile compound profiles (p < 0.05) except for total ketones and carboxylic acids, where higher content was observed in the leaf blade compared to the bulb, regardless of the genotype. These findings highlight WO's potential for use in ready-to-eat products, enhancing its market value.

Real-world Effectiveness and Tolerability of Interferon-free Direct-acting Antiviral for 15,849 Patients with Chronic Hepatitis C: A Multinational Cohort Study.

As practice patterns and hepatitis C virus (HCV) genotypes (GT) vary geographically, a global real-world study from both East and West covering all GTs can help inform practice policy toward the 2030 HCV elimination goal. This study aimed to assess the effectiveness and tolerability of DAA treatment in routine clinical practice in a multinational cohort for patients infected with all HCV GTs, focusing on GT3 and GT6. We analyzed the sustained virological response (SVR12) of 15,849 chronic hepatitis C patients from 39 Real-World Evidence from the Asia Liver Consortium for HCV clinical sites in Asia Pacific, North America, and Europe between 07/01/2014-07/01/2021. The mean age was 62±13 years, with 49.6% male. The demographic breakdown was 91.1% Asian (52.9% Japanese, 25.7% Chinese/Taiwanese, 5.4% Korean, 3.3% Malaysian, and 2.9% Vietnamese), 6.4% White, 1.3% Hispanic/Latino, and 1% Black/African-American. Additionally, 34.8% had cirrhosis, 8.6% had hepatocellular carcinoma (HCC), and 24.9% were treatment-experienced (20.7% with interferon, 4.3% with direct-acting antivirals). The largest group was GT1 (10,246 [64.6%]), followed by GT2 (3,686 [23.2%]), GT3 (1,151 [7.2%]), GT6 (457 [2.8%]), GT4 (47 [0.3%]), GT5 (1 [0.006%]), and untyped GTs (261 [1.6%]). The overall SVR12 was 96.9%, with rates over 95% for GT1/2/3/6 but 91.5% for GT4. SVR12 for GT3 was 95.1% overall, 98.2% for GT3a, and 94.0% for GT3b. SVR12 was 98.3% overall for GT6, lower for patients with cirrhosis and treatment-experienced (TE) (93.8%) but ≥97.5% for treatment-naive patients regardless of cirrhosis status. On multivariable analysis, advanced age, prior treatment failure, cirrhosis, active HCC, and GT3/4 were independent predictors of lower SVR12, while being Asian was a significant predictor of achieving SVR12. In this diverse multinational real-world cohort of patients with various GTs, the overall cure rate was 96.9%, despite large numbers of patients with cirrhosis, HCC, TE, and GT3/6. SVR12 for GT3/6 with cirrhosis and TE was lower but still excellent (>91%).

Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals.

Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes and >90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy and global HCV elimination. We characterized HCV subtypes "rare" in the United Kingdom (non-1a/1b/2b/3a/4d) by means of whole-genome sequencing via a national surveillance program. Genetic analyses to determine the genotype of samples with unresolved genotypes were undertaken by comparison with International Committee on Taxonomy of Viruses HCV reference sequences. Two HCV variants were characterized as being closely related to the recently identified genotype (GT) 8, with >85% pairwise genetic distance similarity to GT8 sequences and within the typical intersubtype genetic distance range. The individuals infected by the variants were UK residents originally from Pakistan and India. In contrast, a third variant was only confidently identified to be more similar to GT6 compared with other genotypes across 6% of the genome and was isolated from a UK resident originally from Guyana. All 3 were cured with pangenotypic direct-acting antivirals (sofosbuvir-velpatasvir or glecaprevir-pibrentasvir) despite the presence of resistance polymorphisms in NS3 (80K/168E), NS5A (28V/30S/62L/92S/93S) and NS5B (159F). This study expands our knowledge of HCV diversity by identifying 2 new GT8 subtypes and potentially a new genotype.

Real-life effectiveness of sofosbuvir/velpatasvir/voxilaprevir in hepatitis C patients previously treated with sofosbuvir/velpatasvir or glecaprevir/pibrentasvir.

Sofosbuvir, velpatasvir and voxilaprevir (SOF/VEL/VOX) is the recommended rescue therapy for patients with chronic hepatitis C infection who fail direct-acting antivirals (DAAs). Data are limited on the effectiveness of this treatment after the current first-line therapies. Our aim was to analyse the effectiveness and safety of SOF/VEL/VOX among patients failing sofosbuvir/velpatasvir (SOF/VEL) or glecaprevir/pibrentasvir (GLE/PIB). Retrospective multicentre study (26 Spanish hospitals), including chronic hepatitis C patients unsuccessfully treated with SOF/VEL or GLE/PIB, and retreated with SOF/VEL/VOX ± ribavirin for 12 weeks between December 2017 and December 2022. In total, 142 patients included: 100 (70.4%) had failed SOF/VEL and 42 (29.6%) GLE/PIB. Patients were mainly men (84.5%), White (93.9%), with hepatitis C virus genotype (GT) 3 (49.6%) and 47.2% had liver cirrhosis. Sustained virological response (SVR) was evaluated in 132 patients who completed SOF/VEL/VOX and were followed 12 weeks after end of treatment; 117 (88.6%) achieved SVR. There were no significant differences in SVR rates according to initial DAA treatment (SOF/VEL 87.9% vs. GLE/PIB 90.2%, p = 0.8), cirrhosis (no cirrhosis 90% vs. cirrhosis 87.1%, p = 0.6) or GT3 infection (non-GT3 91.9% vs. GT3 85.5%, p = 0.3). However, when considering the concurrent presence of SOF/VEL treatment, cirrhosis and GT3 infection, SVR rates dropped to 82.8%. Ribavirin was added in 8 (6%) patients, all achieved SVR. SOF/VEL/VOX is an effective rescue therapy for failures to SOF/VEL or GLE/PIB, with an SVR of 88.6%. Factors previously linked to lower SVR rates, such as GT3 infection, cirrhosis and first-line therapy with SOF/VEL were not associated with lower SVRs.

Comparison of diagnostic performance among Abbott RealTime HCV Genotyping II, Abbott HCV Genotype plus RUO, and Roche Cobas HCV Genotyping assays for hepatitis C virus genotyping.

Comparison of diagnostic accuracy for commercial hepatitis C virus (HCV) genotyping (Abbott RealTime HCV Genotyping II, Roche Cobas Genotyping) and investigational Abbott HCV Genotype plus RUO assays designed to discriminate genotype (GT)-1a, 1b or 6 in cases of ambiguous GT from the Abbott commercial assay remains limited. 743 HCV-viremic samples were subjected to analysis using Abbott and Roche commercial as well as Abbott HCV Genotype plus RUO assays. Next-generation sequencing (NGS) targeting core region was employed as the reference standard. Diagnostic accuracy was reported as the number of participants (percentages) along with 95% confidence intervals (CIs). Using NGS, 741 samples (99.7%) yielded valid genotyping results. The diagnostic accuracies were 97.6% (95% CI: 96.1%-98.5%) and 95.3% (95% CI: 93.4%-96.6%) using Abbott and Roche commercial assays (p = 0.0174). Abbott commercial assay accurately diagnosed HCV GT-6a and 6w, whereas Roche commercial assay accurately diagnosed HCV GT-6a. Both assays demonstrated low accuracies for HCV GT-6b, 6e, 6g, and 6n. Abbott HCV Genotype plus RUO assay discriminated 13 of the 14 samples (92.9%; 95% CI: 64.2%-99.6%) that yielded ambiguous GT. Both assays were capable of diagnosing mixed HCV infections when the minor genotype comprised >8.4% of the viral load. The diagnostic performance of commercial HCV genotyping assays is commendable. Abbott assay demonstrated superior performance compared to Roche assay in diagnosing HCV GT-6. Abbott HCV Genotype plus RUO assay aids in discriminating ambiguous GT. Both commercial assays are proficient in diagnosing mixed HCV infections at a cut-off viral load of 8.4% in minor genotype.

Estimation of First Line Anti-Tubercular Drugs resistance and their genetic analysis by Geno Type MTBDRplus assay from an Intermediate Reference Laboratory in Eastern Uttar Pradesh, India

Estimation of First Line Anti-Tubercular Drugs resistance and their genetic analysis by Geno Type MTBDRplus assay from an Intermediate Reference Laboratory in Eastern Uttar Pradesh, India