From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:
More recently, concerns have been raised that HGT from genetically modified organisms (GMOs) could have adverse effects (Pontiroli et al., 2007). HGT of an introduced gene in a GMO may confer a novel trait in another organism, which could be a source of potential harm to the health of people or the environment. For example, the transfer of antibiotic resistance genes to a pathogen has the potential to compromise human or animal therapy (Bennett et al., 2004), transfer of a viral gene to a non-homologous virus may result in an emerging disease (Falk and Bruening, 1994) or gene transfer to humans has been controversially proposed as a potential trigger for oncogenesis (Ho et al., 2000).
What is a "non-homologous virus"? A virus whose species is the same but the strain is different from the virus taken as the donor for the GMO? Or just any virus (including viruses from different species) whose DNA or RNA sequence is different from the GMO donor virus?
Excuse me if the question seems too simple.