word count: 242 24 Main text word count: 5308 25Abstract 26 27 The PA-X protein of influenza A virus has roles in host cell shut-off and viral pathogenesis. 28While most strains are predicted to encode PA-X, strain-dependent variations in activity have 29 been noted. We found that PA-X protein from A/PR/8/34 (PR8) strain had significantly lower 30 repressive activity against cellular gene expression compared with PA-Xs from the avian 31 strains A/turkey/England/50-92/91 (H5N1) (T/E) and A/chicken/Rostock/34 (H7N1). Loss of 32 normal PA-X expression, either by mutation of the frameshift site or by truncating the X-33 ORF, had little effect on the infectious virus titre of PR8 or PR8 7:1 reassortants with T/E 34 segment 3 grown in embryonated hens' eggs. However, in both virus backgrounds, mutation 35 of PA-X led to decreased embryo mortality and lower overall pathology; effects that were 36 more pronounced in the PR8 strain than the T/E reassortant, despite the low shut-off activity 37 of the PR8 PA-X. Purified PA-X mutant virus particles displayed an increased ratio of HA to 38 NP and M1 compared to their WT counterparts, suggesting altered virion composition. When 39 the PA-X gene was mutated in the background of poorly growing PR8 6:2 vaccine 40 reassortant analogues containing the HA and NA segments from H1N1 2009 pandemic 41 viruses or an avian H7N3 strain, HA yield increased up to 2-fold. This suggests that the PR8 42 PA-X protein may harbour a function unrelated to host cell shut-off and that disruption of the 43 PA-X gene has the potential to improve the HA yield of vaccine viruses. 44 45 IMPORTANCE Influenza A virus is a widespread pathogen that affects both man and a 46 variety of animal species, causing regular epidemics and sporadic pandemics with major 47 public health and economic consequences. A better understanding of virus biology is 48 therefore important. The primary control measure is vaccination, which for humans, mostly 49 relies on antigens produced in eggs from PR8-based viruses bearing the glycoprotein genes of 50 3 interest. However, not all reassortants replicate well enough to supply sufficient virus antigen 51 for demand. The significance of our research lies in identifying that mutation of the PA-X 52 gene in the PR8 strain of virus can improve antigen yield, potentially by decreasing the 53 pathogenicity of the virus in embryonated eggs. 54 55 ectodomain of the CVV glycoprotein genes (13-21), or introducing a wild-type (WT) virus-101 derived segment 2 (21-29). Our approach was to manipulate expression of an accessory 102 protein virulence factor, PA-X (30). Segment 3, encoding PA as the primary gene product, 103 also expresses PA-X by low-level ribosomal shifting into a +1 open reading frame (ORF) 104 termed the X ORF ( Fig 1A) (30). PA-X is a 29 kDa protein that contains the N-terminal 105 endonuclease domain of PA, and in most isolates, a 61 amino acid C-terminus from the X 106 ORF (30-32). It has roles in shutting off host cell protein synthesis and, at the whole animal 107 le...