Challenges to Differentiate Hepatitis C Genotype 1 and 6: Results from A Field-Study in Cambodia
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BRIEF REPORT
Challenges to Differentiate Hepatitis C Genotype 1 and 6: Results from A Field-Study in Cambodia Anja De Weggheleire
. Irith De Baetselier . Sokkab An .
Sylvie Goletti . Vanessa Suin . Sopheak Thai . Sven Francque . Tania Crucitti . Lutgarde Lynen . Steven Van Gucht . Benoıˆt Mukadi Kabamba
Received: January 3, 2020 Ó The Author(s) 2020
ABSTRACT 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 Digital Features To view digital features for this article go to https://doi.org/10.6084/m9.figshare.12328391. A. De Weggheleire (&) I. De Baetselier T. Crucitti L. Lynen Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerp, Belgium e-mail: [email protected] S. An S. Thai Infectious Diseases Department, Sihanouk Hospital Center of Hope, Phnom Penh, Cambodia S. Goletti B. M. Kabamba Clinical Microbiology, Cliniques Universitaires Saint Luc, Brussels, Belgium V. Suin S. Van Gucht Viral Diseases Department, Sciensano, Brussels, Belgium S. Francque Gastroenterology Hepatology, Antwerp University Hospital, Antwerp, Belgium S. Francque Laboratory of Experimental Medicine and Paediatrics, University of Antwerp, Antwerp, Belgium
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 50 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 50 UTR information. Conclusions: HCV genotype 1b and genotype 6 non-a/non-b were most common. With Versant 2.0 (using 50 UTR and core information), genotype classification (1 or 6) remained inconclusive in 15% of samples. The locally available
Infect Dis Ther
method (LightPower assay) failed to identify genotype 6 non-a/non-b, which highlights that methods using 50 UTR information only should not be us
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