The present study compares in parallel the immune responses and protection generated by a PAV3-based vector and a similar AdHu5-based vector using an avian influenza H5N1 disease model of infection. PAV3-based vector expressing the H5N1 HA antigen was able to generate quick and robust immune responses against H5N1. This finding was supported by the rapid induction of improved immediate protection by the PAV3-HA vaccine compared to AdHu5-HA. Interestingly, both vaccines shared similar in vivo expression, suggesting that the increase in vaccine efficacy observed with PAV3-HA may be due to specific interactions with the immune system rather than enhanced expression of the antigen. A recent study suggests that PAV3-HA may activate different innate immune pathways to AdHu5-HA [30] . Additionally, the PAV3-HA offered improved long-term protection against lethal H5N1 virus challenge with higher levels of detectable antibodies by HI assay. Although full short-term (28 day) survival was observed following vaccination with PAV3-HA or AdHu5-HA at the 10 9 vp/mouse dose, greater weight loss was observed with the AdHu5-HA vaccine. Comparing HI and NAB antibody titres with observed clinical outcome, this suggests that there may have been incomplete neutralization of the virus following vaccination with AdHu5-HA, perhaps explaining why there were differences in the levels of protection observed following challenge 1-year post-vaccination. It has been shown that levels of neutralizing antibodies in serum decrease over time following H5N1 infection [31] . Following vaccination, the exact levels of neutralizing antibodies correlating with full protection from infection with homologous virus is still uncertain. In comparison with total IgG antibody levels, neutralizing antibody titres correlated better with early and long-term protection, similar to previously described reports [19, 32, 33] .