53 Review www.expert-reviews.com ISSN 1473-7159 © 2011 Expert Reviews Ltd 10.1586/ERM.10.101 Hepatitis C virus (HCV) is a blood-borne pathogen that infects approximately 170 mil- lion patients worldwide [101] . Approximately 75–85% of infected patients will become chroni- cally infected. Most patients with chronic HCV are asymptomatic and can lead a normal life. However, in approximately 20% of chronically infected patients, the disease will progress, over a period of 10–30 years, into fibrosis, cirrhosis and possibly hepatocellular carcinoma (HCC), making HCV the leading cause of liver trans- plants [1] . Currently, HCV-infected patients are treated by either pegylated interferon (PEG- IFN) or a combination of PEG-IFN and riba- virin (RBV). Standard regimens include PEG- IFN- a 2b at 1.5 µg/kg per week plus RBV at 800–1400 mg/day, or PEG-IFN- a 2a at a dose of 180 µg/week plus RBV at a dose of 1000– 1200 mg/day; serious adverse events are observed in approximately 10% of treated patients [2] . Patients are considered cured when they have achieved sustained virological response (SVR) after 24 weeks of the end of treatment [102,103] . When patients with genotypes 2 and 3 are treated with combination therapy, they achieve nearly 80% SVR, whereas genotype 1 HCV-infected patients achieve approximately 40–50% SVR [2,3] . Data for HCV-infected patients with geno- types 4, 5 and 6 are currently limited. Patients with genotype 4 who receive combination therapy are reported to achieve 50% SVR [4] . The HCV is a positive-strand RNA virus, with a genome of approximately 9.5 kb, which encodes a large polyprotein of approximately 3033 amino acids. The processing and cleav- age of the polyprotein is carried out using the machinery of the host and viral enzymes, yield- ing approximately ten proteins [5] . HCV mutates constantly owing to the lack of efficient proof reading by RNA polymerase and the lack of 5´–3´ exonuclease activity, which helps the virus to evade the immune system [6] . There are six major genotypes of HCV worldwide, which show more than 30% sequence variation. These genotypes are further classified into subtypes, isolates and quasispecies [7] . Biochemical markers, such as alanine aminotransferase (ALT) and aspartate amino- transferase (AST), may be elevated in the blood of HCV patients and indicate the need for fur- ther testing. However, 40% of infected patients can have normal levels of ALT and aspartate aminotransferase, making these enzymes of low significance in the diagnosis of HCV [8] . Reem R Al Olaby 1 and Hassan ME Azzazy †1 1 The American University in Cairo, 113 Kasr El-Aini Street, Cairo 11511, Egypt † Author for correspondence: Tel.: +2 022 615 2543 Fax: +2 022 795 7565 hazzazy@aucegypt.edu Molecular diagnostic assays represent a cornerstone in the management of hepatitis C virus (HCV) patients. Qualitative and quantitative HCV molecular assays are used for the diagnosis of acute and chronic HCV infections, viral genotyping, viral-load determination, treatment monitoring and prognosis. Reverse-transcription PCR, transcription-mediated amplification and branched DNA amplification are commonly employed for detection of HCV RNA. Recently, new HCV molecular assays that employ nanostructures have emerged and have been proposed as suitable for both low- and high-resource settings, without sacrificing sensitivity and specificity. This article will present current and future HCV molecular diagnostic assays with a focus on their clinical applications. KEYWORDS: branched DNA • genotyping • gold nanoparticle • hepatitis C virus • molecular diagnostics • nanotechnology • PCR • quantum dot • transcription-mediated amplification Hepatitis C virus RNA assays: current and emerging technologies and their clinical applications Expert Rev. Mol. Diagn. 11(1), 53–64 (2011) Author Proof