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Title: Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history
Authors: Zhu, Y.O
Aw, P.P.K
de Sessions, P.F
Hong, S
See, L.X
Hong, L.Z
Wilm, A
Li, C.H
Hue, S
Lim, S.G 
Nagarajan, N 
Burkholder, W.F
Hibberd, M 
Keywords: lamivudine
analytical error
antiviral resistance
antiviral therapy
chronic hepatitis B
controlled study
gene dosage
Hepatitis B virus
microbial diversity
population dynamics
sequence analysis
virus mutation
amino acid substitution
DNA barcoding
drug effect
gene frequency
hepatitis B
Hepatitis B virus
isolation and purification
molecular evolution
virus genome
Amino Acid Substitution
Computational Biology
DNA Barcoding, Taxonomic
Drug Resistance, Viral
Evolution, Molecular
Gene Frequency
Genome, Viral
Hepatitis B
Hepatitis B virus
Issue Date: 2017
Citation: Zhu, Y.O, Aw, P.P.K, de Sessions, P.F, Hong, S, See, L.X, Hong, L.Z, Wilm, A, Li, C.H, Hue, S, Lim, S.G, Nagarajan, N, Burkholder, W.F, Hibberd, M (2017). Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history. BMC Genomics 18 (1) : 829. ScholarBank@NUS Repository.
Rights: Attribution 4.0 International
Abstract: Background: 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. Results: With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Conclusions: Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history. © 2017 The Author(s).
Source Title: BMC Genomics
ISSN: 14712164
DOI: 10.1186/s12864-017-4217-1
Rights: Attribution 4.0 International
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