Within-host nucleotide diversity of virus populations: insights from next-generation sequencing

Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from N...

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Bibliographic Details
Published in:Infection, genetics and evolution genetics and evolution, 2015-03, Vol.30, p.1-7
Main Authors: Nelson, Chase W, Hughes, Austin L
Format: Article
Language:English
Subjects:
Animals
Genes, Viral - genetics
Genetic Variation - genetics
Genetics, Population
Genome, Viral - genetics
Haplorhini
High-Throughput Nucleotide Sequencing
Humans
Sequence Analysis, DNA
Sequence Analysis, RNA
Virology
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Summary:Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from NGS data without the need for inferring linkage. We discuss the potential usefulness of these data for addressing questions of both practical and theoretical interest, including fundamental questions regarding the effective population sizes of within-host viral populations and the modes of natural selection acting on them.
ISSN:1567-1348
1567-7257
DOI:10.1016/j.meegid.2014.11.026