“Zika” and “West Nile virus” were named before 1950, when things were even more racist-y than they are now. “Ebola” got its name because scientists, including ones from the Centers for Disease Control, decided to name it for a river near the village in the Democratic Republic of Congo (then Zaire) where the first case was discovered. They didn’t want to name it after the village because they didn’t want to stigmatize the people living there.
MERS, or “Middle East Respiratory Syndrome,” was named by the International Committee on Taxonomy of Viruses, which has a Coronavirus Study Group and works with the World Health Organization and researchers. Originally, the name contained “SA” in it because the first reported case was in Saudi Arabia, which pissed off the Saudis (and, it turned out, the real first case was in Jordan), so it was changed.