Not only among the Pygmies also among Bantu and Sudanese groups in this Ituri area IgG is very widespread. I think Ebola is an illness since centuries in this area. Also the mortality in this areas is not as high than for example in West-Africa. And I am sure there are great unknown cases in the dense Congo forest.
Armin Prinz, a former WHO expert for Ebola infections in Central Africa
I'm afraid I can't answer your question but I can direct you towards an article that might help in your search for info.
This article offers some suggestions as to why pygmy populations are seronegative for Marburg more often than might be expected (due to the relatively higher seropositive rates for other filoviruses)...Borchert et al. 2005. pygmy populations Seronegative for Marburg Virus. Emerging Infectious Diseases 11(1):174-177 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294351/
In my fairly extensive reading around the topic of Ebola, I've yet to find an article or evidence which can offer a conclusive answer to your question. One of the many, many intriguing unknowns for the infectious disease world.
thanks for a good question. It is not uncommon that people such as pygmees and other spending much time in the wild nature in the same area get exposed to viruses within the same filovirus family as Ebola, but with much less disease causing properties. Some of these virus strains could be attenuated viruses, and would in best case, function as "natural vaccine" strains that induce immunity without being able to cause severe disease.
This is a common phenomena also with several respiratory tract infections, such as influenzas, parainfluenza , coronaviruses a.s.o