Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms

[1]  J. Miłek,et al.  Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds , 2018, Journal of veterinary research.

[2]  Belinda Barnes,et al.  Assessing the probability of introduction and spread of avian influenza (AI) virus in commercial Australian poultry operations using an expert opinion elicitation , 2018, PloS one.

[3]  M. Ciccozzi,et al.  Think globally, act locally: Phylodynamic reconstruction of infectious bronchitis virus (IBV) QX genotype (GI-19 lineage) reveals different population dynamics and spreading patterns when evaluated on different epidemiological scales , 2017, PloS one.

[4]  G. Franzo,et al.  A novel variant of the infectious bronchitis virus resulting from recombination events in Italy and Spain , 2016, Avian pathology : journal of the W.V.P.A.

[5]  G. Franzo,et al.  Porcine circovirus type 2 (PCV2) evolution before and after the vaccination introduction: A large scale epidemiological study , 2016, Scientific Reports.

[6]  Rebecca Rose,et al.  SERAPHIM: studying environmental rasters and phylogenetically informed movements , 2016, Bioinform..

[7]  M. Cortey,et al.  Effect of different vaccination strategies on IBV QX population dynamics and clinical outbreaks , 2016, Vaccine.

[8]  M. Suchard,et al.  SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. , 2016, Molecular biology and evolution.

[9]  Arndt von Haeseler,et al.  W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis , 2016, Nucleic Acids Res..

[10]  E. Holmes,et al.  S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification , 2016, Infection, Genetics and Evolution.

[11]  O. Pybus,et al.  Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data , 2016, BMC Bioinformatics.

[12]  Hadley Wickham,et al.  Spatial Visualization with ggplot2 , 2016 .

[13]  Andrew Rambaut,et al.  Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) , 2016, Virus evolution.

[14]  Nicola De Maio,et al.  New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation , 2015, PLoS genetics.

[15]  Matthew S. Miller,et al.  Age-dependent immune responses and immune protection after avian coronavirus vaccination , 2015, Vaccine.

[16]  B. Murrell,et al.  RDP4: Detection and analysis of recombination patterns in virus genomes , 2015, Virus evolution.

[17]  J. D. de Wit,et al.  Factors influencing the outcome of infectious bronchitis vaccination and challenge experiments , 2014, Avian pathology : journal of the W.V.P.A.

[18]  G. Franzo,et al.  Continued use of IBV 793B vaccine needs reassessment after its withdrawal led to the genotype's disappearance , 2014, Vaccine.

[19]  David Welch,et al.  Efficient Bayesian inference under the structured coalescent , 2014, Bioinform..

[20]  Marion Koopmans,et al.  Genetic data provide evidence for wind-mediated transmission of highly pathogenic avian influenza. , 2013, The Journal of infectious diseases.

[21]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[22]  K. Katoh,et al.  Improvements in Performance and Usability , 2013 .

[23]  Hadley Wickham,et al.  ggmap: Spatial Visualization with ggplot2 , 2013, R J..

[24]  M. Suchard,et al.  Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. , 2012, Molecular biology and evolution.

[25]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[26]  M. Jackwood.  Review of Infectious Bronchitis Virus Around the World , 2012, Avian diseases.

[27]  A. Handel,et al.  Molecular evolution and emergence of avian gammacoronaviruses , 2012, Infection, Genetics and Evolution.

[28]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[29]  Thomas J. Hagenaars,et al.  Modelling the Wind-Borne Spread of Highly Pathogenic Avian Influenza Virus between Farms , 2012, PloS one.

[30]  Alexei J. Drummond,et al.  Phylogenetic and epidemic modeling of rapidly evolving infectious diseases , 2011, Infection, Genetics and Evolution.

[31]  J. Cook,et al.  Infectious bronchitis virus variants: a review of the history, current situation and control measures , 2011, Avian pathology : journal of the W.V.P.A.

[32]  M. Cecchinato,et al.  Epidemiology and Control of Low Pathogenicity Avian Influenza Infections in Rural Poultry in Italy , 2011, Avian diseases.

[33]  M. Suchard,et al.  Phylogeography takes a relaxed random walk in continuous space and time. , 2010, Molecular biology and evolution.

[34]  M. Valsecchi,et al.  Risk factors for highly pathogenic H7N1 avian influenza virus infection in poultry during the 1999-2000 epidemic in Italy. , 2009, Veterinary journal.

[35]  L. Busani,et al.  Transmission parameters of highly pathogenic avian influenza (H7N1) among industrial poultry farms in northern Italy in 1999-2000. , 2007, Preventive veterinary medicine.

[36]  Armin Elbers,et al.  Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry , 2007, PLoS Comput. Biol..

[37]  Greg Ewing,et al.  Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden , 2006, Evolutionary bioinformatics online.

[38]  G. Garner,et al.  A cross-sectional survey of Australian chicken farms to identify risk factors associated with seropositivity to Newcastle-disease virus. , 2006, Preventive veterinary medicine.

[39]  Sergei L. Kosakovsky Pond,et al.  GARD: a genetic algorithm for recombination detection , 2006, Bioinform..

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

[41]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[42]  D. Cavanagh.  Coronaviruses in poultry and other birds , 2005, Avian pathology : journal of the W.V.P.A.

[43]  J. Stegeman,et al.  Risk factors for the introduction of high pathogenicity Avian Influenza virus into poultry farms during the epidemic in the Netherlands in 2003. , 2005, Preventive veterinary medicine.

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

[45]  M. Colby,et al.  Wind-borne transmission of infectious laryngotracheitis between commercial poultry operations , 2005 .

[46]  P. Britton,et al.  Longitudinal field studies of infectious bronchitis virus and avian pneumovirus in broilers using type-specific polymerase chain reactions. , 1999, Avian pathology : journal of the W.V.P.A.

[47]  M. D. de Jong,et al.  Transmission of infectious bronchitis virus within vaccinated and unvaccinated groups of chickens. , 1998, Avian pathology : journal of the W.V.P.A.

[48]  D. Alexander,et al.  Characterisation of influenza A viruses isolated from turkeys in England during March-May 1979. , 1981, Avian pathology : journal of the W.V.P.A.

[49]  Glass Se,et al.  Isolation of avian influenza virus in Texas. , 1981 .

[50]  D. Halvorson,et al.  Avian influenza in caged laying chickens. , 1980 .

[51]  Easterday Bc,et al.  Avian influenza virus infections. II. Experimental epizootiology of influenza A-turkey-Wisconsin-1966 virus in turkeys. , 1970 .

[52]  R. Cumming.  Studies on Australian infectious bronchitis virus. IV. Apparent farm-to-farm airborne transmission of infectious bronchitis virus. , 1970, Avian diseases.

[53]  D. P. Anderson,et al.  Avian influenza virus infections. II. Experimental epizootiology of influenza A-turkey-Wisconsin-1966 virus in turkeys. , 1970, Avian diseases.