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

Overview of attention for article published in BMC Genomics, October 2017
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Title
Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history
Published in
BMC Genomics, October 2017
DOI 10.1186/s12864-017-4217-1
Pubmed ID
Authors

Yuan O. Zhu, Pauline P. K. Aw, Paola Florez de Sessions, Shuzhen Hong, Lee Xian See, Lewis Z. Hong, Andreas Wilm, Chen Hao Li, Stephane Hue, Seng Gee Lim, Niranjan Nagarajan, William F. Burkholder, Martin Hibberd

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. 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. 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 27 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 27 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 5 19%
Researcher 5 19%
Student > Bachelor 4 15%
Student > Ph. D. Student 3 11%
Other 2 7%
Other 4 15%
Unknown 4 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 26%
Agricultural and Biological Sciences 5 19%
Medicine and Dentistry 3 11%
Immunology and Microbiology 2 7%
Computer Science 1 4%
Other 3 11%
Unknown 6 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 February 2018.
All research outputs
#18,575,277
of 23,007,053 outputs
Outputs from BMC Genomics
#8,226
of 10,693 outputs
Outputs of similar age
#251,532
of 328,360 outputs
Outputs of similar age from BMC Genomics
#157
of 202 outputs
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