Research output: Contribution to journal › Article › Academic › peer-review
A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants. / Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V. et al.
In: Journal of virological methods, Vol. 219, 2015, p. 28-37.Research output: Contribution to journal › Article › Academic › peer-review
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TY - JOUR
T1 - A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants
AU - Ho, Cynthia K. Y.
AU - Welkers, Matthijs R. A.
AU - Thomas, Xiomara V.
AU - Sullivan, James C.
AU - Kieffer, Tara L.
AU - Reesink, Henk W.
AU - Rebers, Sjoerd P. H.
AU - de Jong, Menno D.
AU - Schinkel, Janke
AU - Molenkamp, Richard
PY - 2015
Y1 - 2015
N2 - We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing
AB - We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing
U2 - 10.1016/j.jviromet.2015.03.018
DO - 10.1016/j.jviromet.2015.03.018
M3 - Article
C2 - 25818622
VL - 219
SP - 28
EP - 37
JO - Journal of virological methods
JF - Journal of virological methods
SN - 0166-0934
ER -
ID: 2598395