Genotyping Hepatitis C Virus

The Hepatitis C virus (HCV) is a single-stranded RNA virus, with a genome of 9,500 nucleotides. The prevalence of HCV among the general population of Ethiopia is not known. Nonetheless, the impression at the lab is that prevalence is high. Egypt is know to have one of the highest HCV prevalence in the world. It is postulated that this is the result of mass treatment with praziquantel for schistosomiasis using contaminated syringes in the past. Mass treatment against schistosomiasis also occurred in Ethiopia, however, oral treatment were used. Intravenous drug users are also unknown of. Would it be facial tattoos, high number of cesarians, blood transfusions? The primarily mode of transmission is still a mystery.

About 75 – 85% of HCV-infected individuals develop chronic hepatitis, with up to 20% of chronically infected individuals developing cirrhosis. In patients with cirrhosis, the incidence of hepatocellular carcinoma is 1 – 4% per year. Genotype 1 and genotype 4 responds less well to interferon-based anti-HCV drug treatment than genotypes 2 and 3, especially in patients of African descent. Therefore, genotyping of HCV is recommended before the start of antiviral therapy.

Thanks to the lobbying of, among other PharmAccess, treatment for HCV is becoming more affordable in developing countries. Still, hepatitis C viral loads and genotyping is mandatory for managing the treatment.

The Abbott RealTime HCV genotype II assay is an RT-PCR assay for use with the Abbott mSample Preparation System reagents and with the Abbott m2000sp and m2000rt instruments for viral count and genotyping of the viral (HCV) RNA in human blood, serum plasma (EDTA) or tissue donors of HCV-infected individuals. The Abbott RealTime HCV assay is intended for use as an aid in the management of HCV-infected patients undergoing antiviral therapy. The assay measures HCV RNA levels at baseline and during treatment and can be utilized to predict sustained and non-sustained virological response to HCV therapy.

During the verification tests, some remarkable observations were made. There was failure of the internal controls and mismatch at low viral loads. But that’s not the interesting one.

The genotype 4e at the reference laboratory in Germany (most likely they use the Roche system) corresponds with a genotype 1 & 4 double reaction at our lab in Addis Ababa. Genotype 4e is a strain of which little is known. There are only few and partial RNA sequences available for this genotype. It is therefore hypothesized that the primers/probes for gt1 detection from the Abbott assay cross match with genotype 4e.

HCV genotyping


In case, with the Abbott system, a reaction occurs in which both genotype 1 & 4 are detected, the results should be interpreted as HCV genotype 4.


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