Our analyses showed that the Indonesian and Malaysian nucleotide sequences were more closely aligned that sequences with each other than they were with the Bangladesh or Indian sequences. This is not unexpected given the demonstrated movement of flying-foxes between peninsular Malaysia and Sumatera across a sea distance of less than 50 km. While it might be argued that the weaker alignment with the Bangladesh and Indian sequences reflects the non-flying-fox origin of the latter, analysis of sequence derived from multiple species in Malaysia suggests distinct geographic clades. Sequence comparison across a larger portion of the genome, and from a broader geographic footprint across Indonesia is needed to determine the extent of genetic diversity in Indonesian flyingfoxes, especially East Indonesia. The serology findings corroborate those of Johara et al, 2001, Sendow et al, 2006 and Rahman et al 2013 and indicate that Nipah virus and potentially cross-reacting henipaviruses are endemic in P. vampyrus across their geographic range. Sensitivity is often reported in terms of plaque forming units but it is difficult to estimate how many virions form 1 pfu. Sellner estimated that one Vero cell pfu may contain 100- 1000 virions but noted virion number is affected by cell type used. To overcome this problem we determined sensitivity by the absolute quantification of test samples extrapolated from the plasmid standard curve. Using this method we determined the limit of detection to be 16 genome equivalents. Investigations undertaken during the 1995 outbreak in NSW suggested that the viraemia in BFV infection in humans is shortlived, based on the observation that virus could not be cultured from samples with detectable neutralising antibody. Interestingly the PCR-positive sample from 2010 was culture negative, contained high levels of IgM and neutralising antibody but low levels of IgG antibody, consistent with early infection. This suggests that the PCR is capable of detecting virus, at least early in the course of infection. The fact that it was only positive on the second round PCR suggests that the virus was present at a low level. This indicates that the period during which infection can be detected by RT-PCR, is longer than tissue culture allows. It is unlikely that PCR will replace serology as the mainstay of BFV diagnostics as evidenced by the 52 PCR negative clinically suspected and serologically confirmed cases – but it will be a useful adjunct in diagnosing early BFV infection. Sequencing the PCR product from positive samples will allow investigation of strain variation which may provide useful epidemiologic insights into this uniquely Australian alphavirus. Biomarkers have been broadly used to aid in the diagnosis, prognostication or therapy of many medical conditions. Creactive protein is an acute phase protein that plays a prominent role in many diseases.