Literature DB >> 25481279

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

Chase W Nelson1, Austin L Hughes2.   

Abstract

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.
Copyright © 2014 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Next-generation sequencing; Nonsynonymous substitution; Nucleotide diversity; Quasispecies; Synonymous

Mesh：

Year:  2014        PMID： 25481279      PMCID： PMC4316684          DOI： 10.1016/j.meegid.2014.11.026

Source DB:  PubMed          Journal:  Infect Genet Evol        ISSN： 1567-1348            Impact factor:   3.342


  42 in total

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Authors:  Marco Vignuzzi; Jeffrey K Stone; Jamie J Arnold; Craig E Cameron; Raul Andino
Journal:  Nature       Date:  2005-12-04       Impact factor: 49.962

3.  Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus.

Authors:  Austin L Hughes; Shelby O'Connor; Dawn M Dudley; Benjamin J Burwitz; Benjamin N Bimber; David O'Connor
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5.  Widespread purifying selection at polymorphic sites in human protein-coding loci.

Authors:  Austin L Hughes; Bernice Packer; Robert Welch; Andrew W Bergen; Stephen J Chanock; Meredith Yeager
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-05       Impact factor: 11.205

6.  PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.

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Journal:  PLoS One       Date:  2011-01-06       Impact factor: 3.752

7.  Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time.

Authors:  Hui Li; Austin L Hughes; Nazneen Bano; Susan McArdle; Stephen Livingston; Heike Deubner; Brian J McMahon; Lisa Townshend-Bulson; Rachel McMahan; Hugo R Rosen; David R Gretch
Journal:  PLoS One       Date:  2011-05-05       Impact factor: 3.240

8.  Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.

Authors:  Gabriella Rozera; Isabella Abbate; Alessandro Bruselles; Crhysoula Vlassi; Gianpiero D'Offizi; Pasquale Narciso; Giovanni Chillemi; Mattia Prosperi; Giuseppe Ippolito; Maria R Capobianchi
Journal:  Retrovirology       Date:  2009-02-12       Impact factor: 4.602

9.  Quasispecies theory in the context of population genetics.

Authors:  Claus O Wilke
Journal:  BMC Evol Biol       Date:  2005-08-17       Impact factor: 3.260

10.  Hepatitis C virus diversity and evolution in the full open-reading frame during antiviral therapy.

Authors:  Nathan A Cannon; Maureen J Donlin; Xiaofeng Fan; Rajeev Aurora; John E Tavis
Journal:  PLoS One       Date:  2008-05-07       Impact factor: 3.240
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  37 in total

1.  Intrahost Dynamics of Human Cytomegalovirus Variants Acquired by Seronegative Glycoprotein B Vaccinees.

Authors:  Ravit Arav-Boger; Sallie R Permar; Cody S Nelson; Diana Vera Cruz; Melody Su; Guanhua Xie; Nathan Vandergrift; Robert F Pass; Michael Forman; Marie Diener-West; Katia Koelle
Journal:  J Virol       Date:  2019-02-19       Impact factor: 5.103

2.  SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.

Authors:  Chase W Nelson; Louise H Moncla; Austin L Hughes
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3.  Modeling the evolution of SIV sooty mangabey progenitor virus towards HIV-2 using humanized mice.

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Journal:  Virology       Date:  2017-07-24       Impact factor: 3.616

Review 4.  Mixed HCV infection and reinfection in people who inject drugs--impact on therapy.

Authors:  Evan B Cunningham; Tanya L Applegate; Andrew R Lloyd; Gregory J Dore; Jason Grebely
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5.  Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys.

Authors:  Adam L Bailey; Michael Lauck; Ria R Ghai; Chase W Nelson; Katelyn Heimbruch; Austin L Hughes; Tony L Goldberg; Jens H Kuhn; Anna J Jasinska; Nelson B Freimer; Cristian Apetrei; David H O'Connor
Journal:  J Virol       Date:  2016-07-11       Impact factor: 5.103

6.  Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice.

Authors:  Matthew M Hernandez; Audrey Fahrny; Ravi Sachidanandam; Roberto F Speck; Viviana Simon; Anitha Jayaprakash; Gustavo Gers-Huber; Marsha Dillon-White; Annette Audigé; Lubbertus C F Mulder
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7.  HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis.

Authors:  Lisa Mirabello; Meredith Yeager; Kai Yu; Gary M Clifford; Yanzi Xiao; Bin Zhu; Michael Cullen; Joseph F Boland; Nicolas Wentzensen; Chase W Nelson; Tina Raine-Bennett; Zigui Chen; Sara Bass; Lei Song; Qi Yang; Mia Steinberg; Laurie Burdett; Michael Dean; David Roberson; Jason Mitchell; Thomas Lorey; Silvia Franceschi; Philip E Castle; Joan Walker; Rosemary Zuna; Aimée R Kreimer; Daniel C Beachler; Allan Hildesheim; Paula Gonzalez; Carolina Porras; Robert D Burk; Mark Schiffman
Journal:  Cell       Date:  2017-09-07       Impact factor: 41.582

8.  Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys.

Authors:  Cody S Nelson; Diana Vera Cruz; Dollnovan Tran; Kristy M Bialas; Lisa Stamper; Huali Wu; Margaret Gilbert; Robert Blair; Xavier Alvarez; Hannah Itell; Meng Chen; Ashlesha Deshpande; Flavia Chiuppesi; Felix Wussow; Don J Diamond; Nathan Vandergrift; Mark R Walter; Peter A Barry; Michael Cohen-Wolkowiez; Katia Koelle; Amitinder Kaur; Sallie R Permar
Journal:  JCI Insight       Date:  2017-07-06

9.  Increase in the genetic polymorphism of varicella-zoster virus after passaging in in vitro cell culture.

Authors:  Hye Rim Hwang; Seok Cheon Kim; Se Hwan Kang; Chan Hee Lee
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10.  Conditional Immune Escape during Chronic Simian Immunodeficiency Virus Infection.

Authors:  Dane D Gellerup; Alexis J Balgeman; Chase W Nelson; Adam J Ericsen; Matthew Scarlotta; Austin L Hughes; Shelby L O'Connor
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