There has been growing interest in the use of plant biomass, particularly secondary cell walls, as a sustainable feedstock for second generation biofuels. However, the feasibility of converting cellulose and other cell wall carbohydrates into biofuels and other chemicals is hindered by the hydrophobic phenolic polymer, lignin, which makes the secondary cell wall inherently recalcitrant to breakdown and hampers enzymatic hydrolysis. Secondary cell walls with altered composition naturally occur in xylem fibres of âLord Lambourneâ apple trees infected with Apple Rubbery Wood associated Virus (ARWaV). However, the development of symptoms has not been described in detail and the mechanism by which ARWaV modifies the secondary cell wall has never been studied. In this study, a detailed morphological and biochemical assessment of symptoms was performed during symptomatic wood development in branches infected with ARWaV. Symptomatic xylem was characterised by fibres with very thick secondary cell walls and overall, contained a third less lignin and a two-fold higher levels of soluble phenolics, whilst the total cellulose and hemicellulose content remained unchanged. These compositional modifications resulted in a two-fold increase in the glucose released from symptomatic xylem digested with cellulase. Using a systematic biological approach the molecular mechanism that determines secondary cell wall alterations during symptom development, specifically poor lignification was investigated. Proteomic and metabolomics analyses together demonstrated that the first committed stage of lignin biosynthesis, involving the conversion of phenylalanine to cinnamic acid via phenylalanine ammonia lyase, was disrupted in symptomatic xylem. RNA-sequencing analysis was also used to examine transcriptomic changes associated with symptom development. However, gene expression patterns were largely inconsistent with the biochemistry of symptomatic wood and other omics analyses indicating a potential tissue-sampling bias. Functional analysis experiments of apple MYB and NAC transcription factors in the Arabidopsis hypocotyl are also described, revealing potentially novel roles for MYB83 during secondary cell wall formation. Overall, the experiments performed in this study provide a comprehensive analysis of symptom development in the xylem of branches infected with ARWaV.