Adaptive Evolution and Environmental Durability Jointly Structure Phylodynamic Patterns in Avian Influenza Viruses

Avian influenza viruses show high genetic diversity, but give rise to pandemic human influenza strains which are much less diverse; we show that these contrasting degrees of viral diversity can be explained by both host (demography) and viral (environmental durability and mutability) factors.

[1]  Michael Worobey,et al.  A synchronized global sweep of the internal genes of modern avian influenza virus , 2014, Nature.

[2]  Timothy B. Stockwell,et al.  Influenza A Virus Migration and Persistence in North American Wild Birds , 2013, PLoS pathogens.

[3]  Bin Cao,et al.  Human infection with avian influenza A H7N9 virus: an assessment of clinical severity , 2013, The Lancet.

[4]  Trevor Bedford,et al.  Integrating influenza antigenic dynamics with molecular evolution , 2013, eLife.

[5]  C. Webb,et al.  Environmental and Demographic Determinants of Avian Influenza Viruses in Waterfowl across the Contiguous United States , 2012, PloS one.

[6]  Cecile Viboud,et al.  Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza , 2012, Proceedings of the National Academy of Sciences.

[7]  Trevor Bedford,et al.  Canalization of the evolutionary trajectory of the human influenza virus , 2011, BMC Biology.

[8]  Trevor Bedford,et al.  Strength and tempo of selection revealed in viral gene genealogies , 2011, BMC Evolutionary Biology.

[9]  A. Ike,et al.  Persistence of Avian Influenza Viruses in Lake Sediment, Duck Feces, and Duck Meat , 2011, Applied and Environmental Microbiology.

[10]  Pejman Rohani,et al.  An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses , 2011, BMC Bioinformatics.

[11]  Parantu K. Shah,et al.  The dChip survival analysis module for microarray data , 2011, BMC Bioinformatics.

[12]  J. Lennon,et al.  Microbial seed banks: the ecological and evolutionary implications of dormancy , 2011, Nature Reviews Microbiology.

[13]  R. Fouchier,et al.  Dynamics and ecological consequences of avian influenza virus infection in greater white-fronted geese in their winter staging areas , 2010, Proceedings of the Royal Society B: Biological Sciences.

[14]  R. Webster,et al.  Can Preening Contribute to Influenza A Virus Infection in Wild Waterbirds? , 2010, PloS one.

[15]  J. Drake,et al.  A general multi-strain model with environmental transmission: invasion conditions for the disease-free and endemic states. , 2010, Journal of theoretical biology.

[16]  Trevor Hastie,et al.  Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.

[17]  M. S. Beato,et al.  Unexpected heat resistance of Italian low-pathogenicity and high-pathogenicity avian influenza A viruses of H7 subtype to prolonged exposure at 37°C , 2009, Avian pathology : journal of the W.V.P.A.

[18]  Edward C. Holmes,et al.  Discovering the Phylodynamics of RNA Viruses , 2009, PLoS Comput. Biol..

[19]  J. Guégan,et al.  Water-borne transmission drives avian influenza dynamics in wild birds: the case of the 2005-2006 epidemics in the Camargue area. , 2009, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[20]  John M Drake,et al.  Environmental transmission of low pathogenicity avian influenza viruses and its implications for pathogen invasion , 2009, Proceedings of the National Academy of Sciences.

[21]  Steve Valeika,et al.  Avian influenza virus in water: infectivity is dependent on pH, salinity and temperature. , 2009, Veterinary microbiology.

[22]  Pejman Rohani,et al.  The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics , 2009, PLoS Comput. Biol..

[23]  Nathan Birnbaum,et al.  Methods for Inactivation of Avian Influenza Virus in the Environment , 2009 .

[24]  Edward C Holmes,et al.  Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds. , 2009, Virology.

[25]  P. Buchy,et al.  Environmental Contamination during Influenza A Virus (H5N1) Outbreaks, Cambodia, 2006 , 2008, Emerging infectious diseases.

[26]  C. Viboud,et al.  Explorer The genomic and epidemiological dynamics of human influenza A virus , 2016 .

[27]  Jonathan A. Runstadler,et al.  The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds , 2008, PLoS pathogens.

[28]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[29]  D. Stallknecht,et al.  Chlorine Inactivation of Highly Pathogenic Avian Influenza Virus (H5N1) , 2007, Emerging infectious diseases.

[30]  D. Stallknecht,et al.  Persistence of H5 and H7 Avian Influenza Viruses in Water , 2007, Avian diseases.

[31]  G. Barigazzi,et al.  Antigenic and Genetic Evolution of Swine Influenza A (H3N2) Viruses in Europe , 2007, Journal of Virology.

[32]  Elizabeth C. Theil,et al.  Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans , 2006, Science.

[33]  I. Capua,et al.  Control of Avian Influenza in Poultry , 2006, Emerging infectious diseases.

[34]  A. Osterhaus,et al.  Avian Flu: Multiple introductions of H5N1 in Nigeria , 2006, Nature.

[35]  Mark A. Miller,et al.  Synchrony, Waves, and Spatial Hierarchies in the Spread of Influenza , 2006, Science.

[36]  A. Osterhaus,et al.  Global Patterns of Influenza A Virus in Wild Birds , 2006, Science.

[37]  D. Suarez,et al.  Development and Application of Reference Antisera against 15 Hemagglutinin Subtypes of Influenza Virus by DNA Vaccination of Chickens , 2006, Clinical and Vaccine Immunology.

[38]  D. Butler.  Yes, but will it jump? , 2006, Nature.

[39]  Bryan T Grenfell,et al.  Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses , 2005, PLoS biology.

[40]  Y. Guan,et al.  Avian flu: H5N1 virus outbreak in migratory waterfowl , 2005, Nature.

[41]  O. Pybus,et al.  Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.

[42]  P. Palese,et al.  Influenza: old and new threats , 2004, Nature Medicine.

[43]  R. Webster,et al.  Influenza A viruses of migrating wild aquatic birds in North America. , 2004, Vector borne and zoonotic diseases.

[44]  O. Pybus,et al.  Unifying the Epidemiological and Evolutionary Dynamics of Pathogens , 2004, Science.

[45]  N. Ferguson,et al.  Ecological and immunological determinants of influenza evolution , 2003, Nature.

[46]  Bryan T Grenfell,et al.  Dynamics and selection of many-strain pathogens , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[47]  M. Bowler,et al.  Coexistence and relative abundance in forest trees , 2002, Nature.

[48]  Edward C. Holmes,et al.  Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis , 2002, Journal of Molecular Evolution.

[49]  W. J. Bean,et al.  Coinfection of wild ducks by influenza A viruses: distribution patterns and biological significance , 1997, Journal of virology.

[50]  R. Webster,et al.  Biological and molecular characterization of H13N2 influenza type A viruses isolated from turkeys and surface water. , 1993, Avian diseases.

[51]  R. Webster,et al.  Evolution and ecology of influenza A viruses. , 1992, Current topics in microbiology and immunology.

[52]  D. Stallknecht,et al.  Effects of pH, temperature, and salinity on persistence of avian influenza viruses in water. , 1990, Avian diseases.

[53]  K. Shortridge,et al.  Possible waterborne transmission and maintenance of influenza viruses in domestic ducks , 1982, Applied and environmental microbiology.

[54]  P. Chesson,et al.  Environmental Variability Promotes Coexistence in Lottery Competitive Systems , 1981, The American Naturalist.

[55]  W. J. Bean,et al.  Intestinal influenza: Replication and characterization of influenza viruses in ducks , 1978, Virology.

[56]  Timothy B. Stockwell,et al.  Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. , 2012, Ecology letters.

[57]  Alexei J Drummond,et al.  Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. , 2006, Molecular biology and evolution.

[58]  Gary Adam Zeitlin,et al.  Avian Influenza , 2005, Current infectious disease reports.

[59]  N. Cox,et al.  Global epidemiology of influenza: past and present. , 2000, Annual review of medicine.

[60]  R. Tibshirani.  Regression Shrinkage and Selection via the Lasso , 1996 .

[61]  R. Webster,et al.  Water-bone transmission of influenza A viruses? , 1979, Intervirology.