Comparison of cobas HCV GT against Versant HCV Genotype 2.0 (LiPA) with confirmation by Sanger sequencing

Autor: H. Lee, Tracy Si-Yu Png, Guan Huei Lee, Cui Wen Chua, Lily Chiu, Falah Yusrina, Chun Kiat Lee, Mui Joo Khoo, Gabriel Yan, Benedict Yan
Rok vydání: 2018
Předmět:
Zdroj: Journal of Virological Methods. 255:8-13
ISSN: 0166-0934
DOI: 10.1016/j.jviromet.2018.02.004
Popis: Background : Correct identification of infecting hepatitis C virus (HCV) genotype is helpful for targeted antiviral therapy. Objectives : Here, we compared the HCV genotyping performance of the cobas HCV GT assay against the Versant HCV Genotype 2.0 (LiPA) assay, using 97 archived serum samples. Study design : In the event of discrepant or indeterminate results produced by either assay, the core and NS5B regions were sequenced. Results : Of the 97 samples tested by the cobas, 25 (26%) were deemed indeterminate. Sequencing analyses confirmed 21 (84%) of the 25 samples as genotype 6 viruses with either subtype 6m, 6n, 6v, 6xa, or unknown subtype. Of the 97 samples tested by the LiPA, thirteen (13%) were deemed indeterminate. Seven (7%) were assigned with genotype 1, with unavailable/inconclusive results from the core region of the LiPA. Notably, the 7 samples were later found to be either genotype 3 or 6 by sequencing analyses. Moreover, 1 sample by the LiPA was assigned as genotypes 4 (cobas: indeterminate) but were later found to be genotype 3 by sequencing analyses, highlighting its limitation in assigning the correct genotype. Conclusions : The cobas showed similar or slightly higher accuracy (100%; 95% CI 94–100%) compared to the LiPA (99%; 95% CI 92–100%). Twenty-six percent of the 97 samples tested by the cobas had indeterminate results, mainly due to its limitation in identifying genotype 6 other than subtypes 6a and 6b. This presents a significant assay limitation in Southeast Asia, where genotype 6 infection is highly prevalent.
Databáze: OpenAIRE
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