Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history

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Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history
Title:
Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history
Journal Title:
BMC Genomics
Keywords:
Publication Date:
27 October 2017
Citation:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4217-1
Abstract:
Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients – once before antiviral treatment and once after viral rebound due to resistance.
License type:
http://creativecommons.org/licenses/by/4.0/
Funding Info:
The work presented here was funded by the Agency of Science, Technology and Research (A*STAR) and the grant JCO CDA 13302FG059. YOZ, PA, PFS, SGL, and MH were also funded by the grant titled Eradication of HBV TCR Program: NMRC/TCR/014-NUHS/2015. NN and WFB were also funded by the grant JCO DP 1334 k00082.
Description:
ISSN:
1471-2164
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