Related Experiment Video
Updated: Dec 20, 2025
A Protocol for Analyzing Hepatitis C Virus Replication
Published on: June 26, 2014
Challenges to Differentiate Hepatitis C Genotype 1 and 6: Results from A Field-Study in Cambodia
Anja De Weggheleire1, Irith De Baetselier2, Sokkab An3
1Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerp, Belgium. adeweggheleire@itg.be.
Insights
Hepatitis C virus (HCV) genotyping in Cambodian coinfected patients revealed genotype 1b and 6 non-a/non-b as most common. Methods relying solely on 5'UTR information are unreliable for Cambodia.
Area of Science:
- Virology
- Infectious Diseases
- Public Health
Background:
- Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) coinfection presents unique challenges in resource-limited settings.
- Accurate HCV genotyping is crucial for effective treatment and epidemiological surveillance.
Purpose of the Study:
- To evaluate the performance and identify challenges of different HCV genotyping methods in a Cambodian HCV/HIV coinfection project.
- To determine the most prevalent HCV genotypes in this specific patient population.
Main Methods:
- HCV genotyping was performed on 106 coinfected patients using LightPower Taqman real-time PCR and Versant 2.0 line probe assay.
- Sequencing of the 5'UTR/core region was used to resolve inconclusive Versant results.
- Performance comparison between the two genotyping methods was conducted.
Main Results:
- Versant 2.0 provided interpretable results for 97.2% of samples, identifying genotypes 1b and 6 non-a/non-b as most common.
- Sequencing confirmed discrepancies, particularly for genotype 6, which was misclassified by the LightPower assay.
- A definitive genotype was assigned to 104 patients, with 1b (44.2%) and 6 non-a/non-b (39.4%) predominating.
Conclusions:
- HCV genotypes 1b and 6 non-a/non-b are the most prevalent in Cambodian HCV/HIV coinfected patients.
- The Versant 2.0 assay, utilizing both 5'UTR and core regions, is more reliable than methods using only 5'UTR information.
- National guidelines should recommend genotyping methods that include core region analysis for accurate HCV identification in Cambodia.
Introduction:
We aim to report on results and challenges of different methods used for hepatitis C (HCV) genotyping in a Cambodian HCV/HIV coinfection project.
Methods:
Samples of 106 patients were available. HCV genotyping was initially (63 samples) done by the LightPower Taqman real-time PCR method (Viet A Corp.) and quality controlled using the Versant 2.0 line probe assay (Siemens Healthcare). Next, following interim quality control results, all 106 samples were (re)genotyped with Versant 2.0, complemented with 5'UTR/core sequencing for uninterpretable/incomplete Versant results.
Results:
Using Versant, 103 (97.2%) of the 106 HCV-coinfected patients had an interpretable genotype result: 1b (50.5%), 6 non-a/non-b (30.1%), 1a (6.8%), 6a or b (4.9%), 2 (3.9%), 1 (2.9%) and 3 (1.0%). For 16 samples that were interpreted as genotype 1 or 1b per Versant's current instructions, it could not be excluded that it concerned a genotype 6 infection as the core region line patterns on the Versant test strip were unavailable, inconclusive or atypical. Upon sequencing, seven of these were genotyped as 1b and nine as genotype 6. Combining Versant and sequencing results, a definitive genotype was assigned in 104 patients: 1b (44.2%), 6 non-a/non-b (39.4%), 1a (6.7%), 6a or b (4.8%), 2 (3.8%) and 3 (1.0%). Genotyping by LightPower and Versant was discordant for 23 (of 63) samples. The LightPower assay misclassified all genotype 6 non-a/non-b samples as genotype 1, which indicates that this assay is only using 5'UTR information.
Conclusions:
HCV genotype 1b and genotype 6 non-a/non-b were most common. With Versant 2.0 (using 5'UTR and core information), genotype classification (1 or 6) remained inconclusive in 15% of samples. The locally available method (LightPower assay) failed to identify genotype 6 non-a/non-b, which highlights that methods using 5'UTR information only should not be used in Cambodia. Regional/national guidelines should be explicit about this.
Trial Registration:
This study was performed as part of a larger cross-sectional study on the burden of hepatitis C coinfection in HIV patients in Cambodia (Clinical.trials.gov: HCV-Epi NCT02361541).
