Please use this identifier to cite or link to this item: https://doi.org/10.1186/s12864-017-4217-1
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dc.titleSingle-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history
dc.contributor.authorZhu, Y.O
dc.contributor.authorAw, P.P.K
dc.contributor.authorde Sessions, P.F
dc.contributor.authorHong, S
dc.contributor.authorSee, L.X
dc.contributor.authorHong, L.Z
dc.contributor.authorWilm, A
dc.contributor.authorLi, C.H
dc.contributor.authorHue, S
dc.contributor.authorLim, S.G
dc.contributor.authorNagarajan, N
dc.contributor.authorBurkholder, W.F
dc.contributor.authorHibberd, M
dc.date.accessioned2020-10-27T10:19:24Z
dc.date.available2020-10-27T10:19:24Z
dc.date.issued2017
dc.identifier.citationZhu, 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. https://doi.org/10.1186/s12864-017-4217-1
dc.identifier.issn14712164
dc.identifier.urihttps://scholarbank.nus.edu.sg/handle/10635/181242
dc.description.abstractBackground: 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).
dc.rightsAttribution 4.0 International
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceUnpaywall 20201031
dc.subjectlamivudine
dc.subjectlamivudine
dc.subjectadaptation
dc.subjectanalytical error
dc.subjectantiviral resistance
dc.subjectantiviral therapy
dc.subjectArticle
dc.subjectchronic hepatitis B
dc.subjectcontrolled study
dc.subjectdemography
dc.subjectevolution
dc.subjectgene dosage
dc.subjectHepatitis B virus
dc.subjecthuman
dc.subjectmicrobial diversity
dc.subjectnonhuman
dc.subjectpopulation dynamics
dc.subjectsequence analysis
dc.subjectvirion
dc.subjectvirus mutation
dc.subjectallele
dc.subjectamino acid substitution
dc.subjectbiology
dc.subjectDNA barcoding
dc.subjectdrug effect
dc.subjectgene frequency
dc.subjectgenetics
dc.subjecthepatitis B
dc.subjectHepatitis B virus
dc.subjectisolation and purification
dc.subjectmolecular evolution
dc.subjectmutation
dc.subjectprocedures
dc.subjectvirology
dc.subjectvirus genome
dc.subjectAlleles
dc.subjectAmino Acid Substitution
dc.subjectComputational Biology
dc.subjectDNA Barcoding, Taxonomic
dc.subjectDrug Resistance, Viral
dc.subjectEvolution, Molecular
dc.subjectGene Frequency
dc.subjectGenome, Viral
dc.subjectHepatitis B
dc.subjectHepatitis B virus
dc.subjectHumans
dc.subjectLamivudine
dc.subjectMutation
dc.subjectVirion
dc.typeArticle
dc.contributor.departmentMEDICINE
dc.contributor.departmentMICROBIOLOGY AND IMMUNOLOGY
dc.description.doi10.1186/s12864-017-4217-1
dc.description.sourcetitleBMC Genomics
dc.description.volume18
dc.description.issue1
dc.description.page829
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