Apparently Ebola, like Tuberculosis or Lyme bacteria and many known viruses, can remain in your body for years after infection

Ebola Virus RNA detection in Semen More than Two Years after Resolution of Acute Ebola Virus Infection 

Abstract 

Among 149 men who survived Ebola virus disease (EVD) and donated semen 260–1016 days after EVD onset, Ebola virus (EBOV) ribonucleic acid (RNA) was detected in 13 (9%). Of 137 men who donated semen 2 years after EVD onset, 11 (8%) had an EBOV RNA-positive specimen. The mechanism underlying the persistence of EBOV RNA in semen is unclear, and it is unclear whether the detection of viral RNA represents the presence of infectious virus."

As case reports have emerged of Ebola virus persisting in the eyes and genitourinary tract, people began to wonder if there were 'privileged sites' that allowed the Ebola virus to remain intact but dormant in people who had had earlier infections. Now there is additional strong evidence this occurs.

 Ebola RNA was detected in semen in 8% of 137 men who survived an Ebola infection--two years later.  Presumably, like the organisms which cause Lyme Disease, TB, chickenpox and other infections, people may develop recurrent illness if their immune system fails to control persisting, live organisms.

While the presence of RNA is not absolute evidence that live, infectious Ebola virus remains in the bodies of recovered victims, as culture of the virus would be, it is hard to imagine any other scenario to explain this finding.  Especially since shedding of Ebola virus was known to possibly continue for months after an infection, even prior to the 2014 Ebola epidemic.