Title: A near-full length genotypic assay for HCV1b
Authors: Cuypers, Lize ×
Snoeck, Joke
Vrancken, Bram
Kerremans, Lien
Vuagniaux, Grégoire
Verbeeck, Jannick
Nevens, Frederik
Camacho, Ricardo Jorge
Vandamme, Anne-Mieke
Van Dooren, Sonia #
Issue Date: 1-Dec-2014
Publisher: Elsevier/North-Holland Biomedical Press
Series Title: Journal of Virological Methods vol:209 pages:126-135
Article number: 10.1016/j.jviromet.2014.09.009
Abstract: A near-full genome genotypic assay for HCV1b was developed, which may prove useful to investigate antiviral drug resistance, given new combination therapies for HCV1 infection. The assay consists of three partially overlapping PCRs followed by Sanger population or Illumina next-generation sequencing. Seventy-seven therapy-naïve samples, spanning the entire diversity range of currently known HCV1b, were used for optimization of PCRs, of which ten were sequenced using Sanger and of these ten, four using Illumina. The median detection limits for the three regions, 5'UTR-NS2, E2-NS5A and NS4B-NS5B, were 570, 5670 and 56,670IU/ml respectively. The number of Illumina reads mapped varied according to the software used, Segminator II being the best performing (81%). Consensus Illumina and Sanger sequencing results accord largely (0.013% major discordances). Differences were due almost exclusively to a larger number of ambiguities (presumably minority variants) scored by Illumina (1.50% minor discordances). The assay is easy to perform in an equipped laboratory; nevertheless, it was difficult to reach high sensitivity and reproducibility, due to the high genetic viral variability. This assay proved to be suitable for detecting drug resistance mutations and can also be used for epidemiological research, even though only a limited set of samples was used for validation.
ISSN: 0166-0934
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
Department of Microbiology & Immunology - miscellaneous
× corresponding author
# (joint) last author

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