Virus population bottlenecks during within-host progression and host-to-host transmission

Roossinck, 2011, The good viruses: viral mutualistic symbioses, Nature Reviews Microbiology, 9, 99, 10.1038/nrmicro2491

Charlesworth, 2009, Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation, Nature Reviews Genetics, 10, 195, 10.1038/nrg2526

Hull, 2002

Leigh-Brown, 1997, Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population, Proceedings of the National Academy of Sciences of the United States of America, 94, 1862, 10.1073/pnas.94.5.1862

Rouzine, 1999, Linkage disequilibrium test implies a large effective population number for HIV in vivo, Proceedings of the National Academy of Sciences of the United States of America, 96, 10758, 10.1073/pnas.96.19.10758

Ramratnam, 1999, Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis, Lancet, 354, 1782, 10.1016/S0140-6736(99)02035-8

Smith, 2008, Venezuelan equine encephalitis virus in the mosquito vector Aedes taeniorhynchus: infection initiated by a small number of susceptible epithelial cells and a population bottleneck, Virology, 372, 176, 10.1016/j.virol.2007.10.011

Huang, 2008, Influenza A virus neuraminidase limits viral superinfection, Journal of Virology, 82, 4834, 10.1128/JVI.00079-08

Lee, 2005, Dual mechanisms of pestiviral superinfection exclusion at entry and RNA replication, Journal of Virology, 79, 3231, 10.1128/JVI.79.6.3231-3242.2005

Lu, 1994, Superinfection exclusion by T-even-type coliphages, Trends in Microbiology, 2, 137, 10.1016/0966-842X(94)90601-7

Nethe, 2005, Retroviral superinfection resistance, Retrovirology, 2, 52, 10.1186/1742-4690-2-52

Ziebell, 2010, Cross-protection: a century of mystery, Advances in Virus Research, 76, 211, 10.1016/S0065-3527(10)76006-1

Elena, 2008, Experimental evolution of plant RNA viruses, Heredity, 100, 478, 10.1038/sj.hdy.6801088

Moury, 2007, Estimation of the number of virus particles transmitted by an insect vector, Proceedings of the National Academy of Sciences of the United States of America, 104, 17891, 10.1073/pnas.0702739104

Betancourt, 2008, Estimation of the effective number of founders that initiate an infection after aphid transmission of a multipartite plant virus, Journal of Virology, 82, 12416, 10.1128/JVI.01542-08

Takeshita, 2004, Spatial analysis for exclusive interactions between subgroups I and II of Cucumber mosaic virus in cowpea, Virology, 328, 45, 10.1016/j.virol.2004.06.046

Sacristan, 2011, Contact transmission of Tobacco mosaic virus: a quantitative analysis of parameters relevant for virus evolution, Journal of Virology, 85, 4974, 10.1128/JVI.00057-11

Keele, 2008, Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection, Proceedings of the National Academy of Sciences of the United States of America, 105, 7552, 10.1073/pnas.0802203105

Gijsbers, 2012, HIV-1 transmission and viral adaptation to the host, Future Virology, 7, 63, 10.2217/fvl.11.134

Bull, 2011, Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection, PLoS Pathogens, 7, e1002243, 10.1371/journal.ppat.1002243

Bull, 2012, Contribution of intra- and interhost dynamics to norovirus evolution, Journal of Virology, 86, 3219, 10.1128/JVI.06712-11

Jridi, 2006, Distinct viral populations differentiate and evolve independently in a single perennial host plant, Journal of Virology, 80, 2349, 10.1128/JVI.80.5.2349-2357.2006

Li, 2004, Genetic bottlenecks reduce population variation in an experimental RNA virus population, Journal of Virology, 78, 10582, 10.1128/JVI.78.19.10582-10587.2004

Aaskov, 2006, Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes, Science, 311, 236, 10.1126/science.1115030

Murcia, 2010, Intra- and interhost evolutionary dynamics of equine influenza virus, Journal of Virology, 84, 6943, 10.1128/JVI.00112-10

Escriu, 2003, The evolution of virulence in a plant virus, Evolution, 57, 755, 10.1111/j.0014-3820.2003.tb00287.x

Dang, 2004, Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways, Proceedings of the National Academy of Sciences of the United States of America, 101, 632, 10.1073/pnas.0307636100

Schrider, 2010, Gene copy-number polymorphism in nature, Proceedings of the Royal Society B: Biological Sciences, 277, 3213, 10.1098/rspb.2010.1180

Weitz, 2008, Collective decision making in bacterial viruses, Biophysical Journal, 95, 2673, 10.1529/biophysj.108.133694

Mileyko, 2008, Small-scale copy number variation and large-scale changes in gene expression, Proceedings of the National Academy of Sciences of the United States of America, 105, 16659, 10.1073/pnas.0806239105

Kourilsky, 1974, Lysogenization by bacteriophage lambda. III. Multiplicity dependent phenomena occuring upon infection by lambda, Biochimie, 56, 1517, 10.1016/S0300-9084(75)80275-6

Cabot, 2000, Nucleotide and amino acid complexity of hepatitis C virus quasispecies in serum and liver, Journal of Virology, 74, 805, 10.1128/JVI.74.2.805-811.2000

Okamoto, 2001, Heterogeneous distribution of TT virus of distinct genotypes in multiple tissues from infected humans, Virology, 288, 358, 10.1006/viro.2001.1097

Pybus, 2009, Evolutionary analysis of the dynamics of viral infectious disease, Nature Reviews Genetics, 10, 540, 10.1038/nrg2583

Frost, 2001, Genetic drift and within-host metapopulation dynamics of HIV-1 infection, Proceedings of the National Academy of Sciences of the United States of America, 98, 6975, 10.1073/pnas.131056998

Levins, 1969, Some demographic and genetic consequences of environmental heterogeneity for biological control, Bulletin of the Entomological Society of America, 15, 237, 10.1093/besa/15.3.237

Brackney, 2011, West Nile Virus genetic diversity is maintained during transmission by culex pipiens quinquefasciatus mosquitoes, PLoS ONE, 6, e24466, 10.1371/journal.pone.0024466

Gutierrez, 2010, Dynamics of the multiplicity of cellular infection in a plant virus, PLoS Pathogens, 6, e1001113, 10.1371/journal.ppat.1001113

Monsion, 2008, Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization, PLoS Pathogens, 4, e1000174, 10.1371/journal.ppat.1000174

Lim, 2007, Viral quasi-species evolution during hepatitis Be antigen seroconversion, Gastroenterology, 133, 951, 10.1053/j.gastro.2007.06.011

Boeras, 2011, Role of donor genital tract HIV-1 diversity in the transmission bottleneck, Proceedings of the National Academy of Sciences of the United States of America, 108, E1156, 10.1073/pnas.1103764108

Josefsson, 2011, Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule, Proceedings of the National Academy of Sciences of the United States of America, 108, 11199, 10.1073/pnas.1107729108

Gutierrez S, Yvon M, Pirolles E, Garzo E, Fereres A, Michalakis Y, Blanc S: Circulating virus load determines the size of bottlenecks in viral populations progressing within a host. PLoS Pathogens 2012, in press.

Zwart, 2011, One is enough: in vivo effective population size is dose-dependent for a plant RNA virus, PLoS Pathogens, 7, e1002122, 10.1371/journal.ppat.1002122

Fabre, 2012, Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing, PLoS Pathogens, 8, e1002654, 10.1371/journal.ppat.1002654

Sacristan, 2003, Estimation of population bottlenecks during systemic movement of tobacco mosaic virus in tobacco plants, Journal of Virology, 77, 9906, 10.1128/JVI.77.18.9906-9911.2003

French, 2003, Evolution of Wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation, Annual Review of Phytopathology, 41, 199, 10.1146/annurev.phyto.41.052002.095559

Kuss, 2008, Multiple host barriers restrict poliovirus trafficking in mice, PLoS Pathogens, 4, e1000082, 10.1371/journal.ppat.1000082

Blanc, 2011, New research horizons in vector-transmission of plant viruses, Current Opinion in Microbiology, 14, 483, 10.1016/j.mib.2011.07.008

Matthews, 2011, Controlling and coordinating development in vector-transmitted parasites, Science, 331, 1149, 10.1126/science.1198077

Kemal, 2003, HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation, Proceedings of the National Academy of Sciences of the United States of America, 100, 12972, 10.1073/pnas.2134064100

Tapparel, 2011, Rhinovirus genome variation during chronic upper and lower respiratory tract infections, PLoS ONE, 6, e21163, 10.1371/journal.pone.0021163

Wright, 2011, Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing, Journal of Virology, 85, 2266, 10.1128/JVI.01396-10

Chohan, 2005, Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1–V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels, Journal of Virology, 79, 6528, 10.1128/JVI.79.10.6528-6531.2005

Derdeyn, 2004, Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission, Science, 303, 2019, 10.1126/science.1093137

Go, 2011, Characterization of glycosylation profiles of HIV-1 transmitted/founder envelopes by mass spectrometry, Journal of Virology, 85, 8270, 10.1128/JVI.05053-11

Liu, 2008, Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses, Virology, 374, 229, 10.1016/j.virol.2008.01.029

Cicin-Sain, 2005, Frequent coinfection of cells explains functional in vivo complementation between cytomegalovirus variants in the multiply infected host, Journal of Virology, 79, 9492, 10.1128/JVI.79.15.9492-9502.2005

Froissart, 2005, Recombination every day: abundant recombination in a virus during a single multi-cellular host infection, PLoS Biology, 3, e89, 10.1371/journal.pbio.0030089

Levy, 2004, Dynamics of HIV-1 recombination in its natural target cells, Proceedings of the National Academy of Sciences of the United States of America, 101, 4204, 10.1073/pnas.0306764101

Lopez-Ferber, 2003, Defective or effective? Mutualistic interactions between virus genotypes, Proceedings of the Royal Society B: Biological Sciences, 270, 2249, 10.1098/rspb.2003.2498

Zeng, 2010, Decision making at a subcellular level determines the outcome of bacteriophage infection, Cell, 141, 682, 10.1016/j.cell.2010.03.034

Gonzalez-Jara, 2009, The multiplicity of infection of a plant virus varies during colonization of its eukaryotic host, Journal of Virology, 83, 7487, 10.1128/JVI.00636-09

Miyashita, 2010, Estimation of the size of genetic bottlenecks in cell-to-cell movement of soil-borne wheat mosaic virus and the possible role of the bottlenecks in speeding up selection of variations in trans-acting genes or elements, Journal of Virology, 84, 1828, 10.1128/JVI.01890-09

Klappenbach, 2000, rRNA operon copy number reflects ecological strategies of bacteria, Applied and Environment Microbiology, 66, 1328, 10.1128/AEM.66.4.1328-1333.2000

Stevenson, 2004, Life history implications of rRNA gene copy number in Escherichia coli, Applied and Environment Microbiology, 70, 6670, 10.1128/AEM.70.11.6670-6677.2004

DeLuna, 2008, Exposing the fitness contribution of duplicated genes, Nature Genetics, 40, 676, 10.1038/ng.123

Perry, 2007, Diet and the evolution of human amylase gene copy number variation, Nature Genetics, 39, 1256, 10.1038/ng2123