Certain viruses are usually cause certain disease. Usually is not always.
In the current climate of MERS-CoV and H7N9 it's understandable that an uptick in acute respiratory illness cases causes alarm but the odds are in favour of one the usual culprits today.
This event is also a reminder of the great job done by expert public disease diagnostic entities like the CDC during times of disease outbreak. Imagine the number of samples that get sent to the CDC for special investigations then scale that up logarithmically during outbreaks. Realistically, even during a pandemic, to find an answer to the type of infectious agent a patient may have requires many separate tests to be conducted on each sample. Time is needed to receive, log and store each patient specimen, to set up, add to and run the diagnostic methods, to carefully interpret the results, sometimes to repeat or add novel testing methods and then to report the results to an increasingly data-hungry public. There's a lot of specialist work in there - even with high throughput system in place these things take some time. We should remember that when reading headlines like "CDC still 'investigating' mystery illness". The implication could be that there is thumb twiddling going because a press releases doesn't appear as quickly as a pirated TV episode on a torrent site. Be assured that there are many steps in a process that seeks to get it right first time.
On a side note, this makes a great case for enhancing diagnostic testing capacity to detect seasonal and endemic respiratory viruses at the local hospital laboratory level. Its surprising how few labs regularly test for the 150+ known rhinoviruses or the 4 non-SARS/MERS coronaviruses for example - together called common cold viruses.
