The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism

Willet et al. (2022) medRxiv 

Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

Forde et al. (2021) bioRxiv

Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway

Zhou et al. (2021) bioRxiv

Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination

Davis et al. (2021) PLOS Pathog

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and impact on B.1.1.7


Meng et al. (2021) Cell Rep

SARS-CoV-2 variants, spike mutations and immune escape


Harvey et al. (2021) Nat Rev Microbiol

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies


Collier et al. (2021) Nature

Genetic determinants of receptor-binding preference and zoonotic potential of H9N2 avian influenza viruses


Peacock et al. (2021) J Virol

Different environmental gradients associated to the spatiotemporal and genetic pattern of the H5N8 highly pathogenic avian influenza outbreaks in poultry in Italy


Scolamacchia et al. (2021) Transbound Emerg Dis

Spatiotemporal reconstruction and transmission dynamics during the 2016-17 H5N8 highly pathogenic avian influenza epidemic in Italy


Harvey et al. (2021) Transbound Emerg Dis

Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70


Kemp et al. (2020) bioRxiv

Genetic basis of antigenic variation of SAT3 foot-and-mouth disease virus


Maake et al. (2020) Front Vet Sci

Genomic and immunogenic protein diversity of Erysipelothrix rhusiopathiae isolated from pigs in Great Britain: implications for vaccine protection


Forde et al. (2020) Front Microbiol

Improving the identification of antigenic sites in the H1N1 influenza virus through accounting for the experimental structure in a sparse hierarchical Bayesian model


Davies et al. (2019) J Royal Stat Soc C

The molecular basis of antigenic variation among A(H9N2) avian influenza viruses


Peacock et al. (2018) Emerg Microbes Infect

Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses


Goldstein et al. (2017) Microb Genom

A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution


Davies et al. (2017) Comput Stat

Identification of low- and high-impact hemagglutinin amino acid substitutions that drive antigenic drift of influenza A(H1N1) viruses


Harvey et al. (2016) PLOS Pathog

Tracking the antigenic evolution of foot-and-mouth disease virus


Reeve et al. (2016) PLOS ONE

Selecting random effect components in a sparse hierarchical Bayesian model for identifying antigenic variability


Davies et al. (2016) In: Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2015. Lecture Notes in Computer Science

 Sparse Bayesian variable selection for the identification of antigenic variability in the foot-and-mouth disease virus


Davies et al. (2014) JMLR Workshop Conf Proc