Detecting whether genome is genetically engineered?
The definition of a GMO for example UK GMO regulatory bodies (HSE) is strictly the artificial introduction of foreign genetic material using targeted genetic engineering, such as splicing,  genome integration etc... Attenuation for example by serial passage the basis of the yellow fever vaccine, does not count as a GMO. 

The simple answer is look at phylogenetic trees between the GMO strain against the total distribution of isolates. If large regions have been spliced the 'silent mutation rate' looks very different,.because the GMO parent is from a very different environment to the recipient.  The switch in replication rate affects the numbers of 'silent mutation', which is fast in RNA viruses.

If the GMO is a point mutation, ie limited amino acid change then I've actually done this with dengue virus and it is fairly easy because the novel mutation make the GMO 'stick out'.of the phylogeny against all natural mutation patterns. At this point the outlier is tracked back to Genbank where the relavant publication defines the engineered virus.

If you are inferring a conspiracy theory that is a different process and a different discussion, particularly if it is Ebolavirus which is a Category 4 pathogen. The investigation is again within the phylogeny, but in this case the answer is always the isolate is a natural zoonose from a sylvatic (wild) transmission cycle which has spilled over into humans.