HCV Detection, Discrimination, and Genotyping Technologies

Abstract

According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.

Keywords: HCV; RT-PCR; detection; genotyping; nucleic acids; quantification; viral load; viruses.

Figure 1

Phylogenetic tree of hepatitis C virus (HCV) sequences. Left, phylogenetic tree constructed based on core sequences. Right, phylogenetic tree constructed based on NS5B sequences. Subtypes 1a, 2a, 3a, 3b, and 6a are shown with 5 different colors in the phylogenetic tree. (Reproduced with permission from [8]).

Figure 2

Various technologies used for the qualitative and quantitative detection of HCV. RT-PCR, Reverse transcription polymerase chain reaction; NASBA, Nucleic acid sequence-based amplification; TMA, Transcription-mediated amplification; RT-LAMP, Reverse transcription loop-mediated isothermal amplification; RCA, Rolling circle amplification; CNT, Carbon nano-tube.

Figure 3

Single-molecule counting after isothermal amplification using an unmodified cell phone camera. (Reproduced with permission from [52]).

Figure 4

NASBA amplification reaction with the P1 (anti-sense) – P2 (sense) oligonucleotide primer set. The overhang on the P1 encodes the promoter sequence for the T7 RNA polymerase. (Reproduced with permission from [58]).

Figure 5

Loop-mediated amplification method. (Reproduced with permission from [70]).

Figure 6

Single-stranded rolling-circle amplification method. (a) Binding of a circularizable probe with a small gap to the single-stranded DNA target; (b) ligated (padlock) probe, and binding of complementary; (c) rolling-circle amplification of a padlock probe by DNA polymerase. (Reproduced with permission from [76]).

Figure 7

Working principle of Bioelectric Recognition Assay (BERA), a functional principle of an amperometric biosensor. (Reproduced with permission from [80]).

Figure 8

A functional principle of a Piezoelectric biosensor. (Reproduced with permission from [82]).

Figure 9

A functional principle of an amperometric biosensor. (Reproduced with permission from [85]).

Figure 10

Scheme of HCV detection by amperometric DNA biosensor. (Reproduced with permission from [86]).

Figure 11

The colorimetric detection of full-length HCV RNA on unmodified GNPs. (Reproduced with permission from [99]).

Figure 12

Schematic representation of a principle used in gold nanoparticle (GNP)-based detection of HCV. (Reproduced with permission from [100]).

Figure 13

A scheme for the detection of HCV by using GNPs labeled conformation-switched hairpin DNA probe and electrocatalytic signal amplification (Reproduced with permission from [101]).

Figure 14

A scheme of peptide nucleic acid (PNA) functionalized single-walled carbon nanotube (SWCNT) field effect transistor device for the detection of HCV (Reproduced with permission from [102]).

Figure 15

A scheme showing on-chip specific detection of HCV and Mycobacterium tuberculosis (Reproduced from [103]).

Figure 16

The strategy of detection and knockdown of the target gene based on Dz and nGO (Reproduced with permission from [105]).

Figure 17

Schematic representation of signal amplification by branched DNA signal amplification technology (Reproduced with permission from [107]).

Figure 18

Schematic representation of signal amplification by branched DNA signal amplification technology.

Figure 19

Schematic representation of the working principle and the experimental protocol of 6 HCV Genotyping 9G Test (Reproduced with permission from [115]).