The alphabet soup of naming new viruses rivals Pentagonese. AIDS. SARS. MRSA. Where do these names come from? One major source of influence in this area is the International Committee on Taxonomy of Viruses (ICTV).
Their latest innovation is MERS, referring to a new form of coronavirus that was first reported in September, 2012. In the meantime the virus has gone by the various abbreviations hCov-EMC, HCOV, NCoV, and nCoV (the last two referring to a "novel coronavirus").
Coming up with a good name is tricky. It should be descriptive and memorable, but naming a virus after a geographic area has major downsides:
Historically, many infectious disease agents—or the diseases themselves—have been named after the place where they were first found. But increasingly, scientists and public health officials have shied away from that system to avoid stigmatizing a particular country or city. When a serious new type of pneumonia started spreading from Asia in 2003, officials at WHO coined the term severe acute respiratory syndrome (SARS) to prevent the disease from being named "Chinese flu" or something similar. (As it happened, the name ruffled feathers in Hong Kong anyway, because the city's official name is Hong Kong SAR, for special administrative region—a fact that WHO had overlooked.)...
The new name is only a recommendation—one which the study group hopes will be adopted widely but which it has no power to enforce, Gorbalenya says. That's because ICTV has the authority only to classify and name entire virus species
For more, check out this post from Science.