Emergence of a Highly Pathogenic Avian Influenza Virus from a Low-Pathogenic Progenitor

The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA

(2013) Sebastian Maurer-Stroh et al.   Virology Journal

Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks

(2013) Joseph Hughes et al.   PLoS Pathogens

New World Bats Harbor Diverse Influenza A Viruses

(2013) Suxiang Tong et al.   PLoS Pathogens

Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing

(2012) M. Selleri et al.   CLINICAL MICROBIOLOGY AND INFECTION

Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing

(2012) G. Croville et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Selection of variant viruses during replication and transmission of H7N1 viruses in chickens and turkeys

(2012) Munir Iqbal et al.   VIROLOGY

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

(2011) G. J. Baillie et al.   JOURNAL OF VIROLOGY

Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry

(2011) Giovanni Cattoli et al.   VACCINE

Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

(2011) Camille Lebarbenchon et al.   Virology Journal

Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic

(2011) Arnaud Bataille et al.   PLoS Pathogens

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Intracellular Distribution of NS1 Correlates with the Infectivity and Interferon Antagonism of an Avian Influenza Virus (H7N1)

(2010) B. Keiner et al.   JOURNAL OF VIROLOGY

Evolutionary Dynamics of Multiple Sublineages of H5N1 Influenza Viruses in Nigeria from 2006 to 2008

(2010) A. Fusaro et al.   JOURNAL OF VIROLOGY

The effects of control measures on the economic burden associated with epidemics of avian influenza in Italy

(2010) S. Sartore et al.   POULTRY SCIENCE

Evaluation of the risk of neighbourhood infection of H7N1 Highly Pathogenic Avian Influenza in Italy using Q statistic

(2010) Paolo Mulatti et al.   PREVENTIVE VETERINARY MEDICINE

Within-flock transmission of H7N1 highly pathogenic avian influenza virus in turkeys during the Italian epidemic in 1999–2000

(2010) Marian E.H. Bos et al.   PREVENTIVE VETERINARY MEDICINE

Molecular adaptation of an H7N3 wild duck influenza virus following experimental multiple passages in quail and turkey

(2010) Simone Giannecchini et al.   VIROLOGY

Sequence and phylogenetic analysis of H7N3 avian influenza viruses isolated from poultry in Pakistan 1995-2004

(2010) Muhammad A. Abbas et al.   Virology Journal

Modelling the spatial spread of H7N1 avian influenza virus among poultry farms in Italy

(2010) I. Dorigatti et al.   Epidemics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evaluation of interventions and vaccination strategies for low pathogenicity avian influenza: spatial and space–time analyses and quantification of the spread of infection

(2009) P. MULATTI et al.   EPIDEMIOLOGY AND INFECTION

Characterisation of a highly pathogenic influenza A virus of subtype H5N2 isolated from ostriches in South Africa in 2004

(2009) Celia Abolnik et al.   Influenza and Other Respiratory Viruses

Acquisition of a Polybasic Hemagglutinin Cleavage Site by a Low-Pathogenic Avian Influenza Virus Is Not Sufficient for Immediate Transformation into a Highly Pathogenic Strain

(2009) O. Stech et al.   JOURNAL OF VIROLOGY

Single-Reaction Genomic Amplification Accelerates Sequencing and Vaccine Production for Classical and Swine Origin Human Influenza A Viruses

(2009) B. Zhou et al.   JOURNAL OF VIROLOGY

Molecular Determinants of Adaptation of Highly Pathogenic Avian Influenza H7N7 Viruses to Efficient Replication in the Human Host

(2009) E. de Wit et al.   JOURNAL OF VIROLOGY

Highly Pathogenic Avian Influenza Virus Subtype H5N1 in Africa: A Comprehensive Phylogenetic Analysis and Molecular Characterization of Isolates

(2009) Giovanni Cattoli et al.   PLoS One

Zoonotic potential of highly pathogenic avian H7N3 influenza viruses from Pakistan

(2009) Uzma B. Aamir et al.   VIROLOGY

Adaptation and transmission of a duck-origin avian influenza virus in poultry species

(2009) Jinling Li et al.   VIRUS RESEARCH

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

NP, PB1, and PB2 Viral Genes Contribute to Altered Replication of H5N1 Avian Influenza Viruses in Chickens

(2008) J. L. Wasilenko et al.   JOURNAL OF VIROLOGY

The genomic and epidemiological dynamics of human influenza A virus

(2008) Andrew Rambaut et al.   NATURE

Risk factors for highly pathogenic H7N1 avian influenza virus infection in poultry during the 1999–2000 epidemic in Italy

(2008) Luca Busani et al.   VETERINARY JOURNAL

Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia

(2008) Tommy Tsan-Yuk Lam et al.   PLoS Pathogens

Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses

(2008) Dhanasekaran Vijaykrishna et al.   PLoS Pathogens

Evidence of Infection by H5N2 Highly Pathogenic Avian Influenza Viruses in Healthy Wild Waterfowl

(2008) Nicolas Gaidet et al.   PLoS Pathogens

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION