A synthetic pathogen was a virus that has been genetically-engineered from a biological precursor.
Following their assimilation by the Borg in the 2370s, the survivors of Species 6339 created a synthetic pathogen that would attack Borg computer programs. The pathogen was carried within 13 of their people, who allowed themselves to be assimilated so that it would be spread to the ship's vinculum. From there, it caused all drones within range to experience the Borg equivalent of multiple personality disorder, eventually leading to their self-destruction. The process would be repeated when another Borg vessel retrieved the vinculum, and so on.
In 2375, Seven of Nine began suffering the effects of the anomalous neural interlink frequency of the infected vinculum. The USS Voyager crew was able to deactivate the vinculum before it caused critical harm. (VOY: "Infinite Regress")