No, you read it.>CDC encourages laboratories to consider adoption of a multiplexed method
Multiplexed means simultaneous detection of two or more substances from a single sample.
Adoption means choosing to take up some activity.
Laboratories were not using a multiplexed method before.>that
pronoun: referring to a specific thing previously mentioned. In this case, the multiplexed method. The next clause is going to tell us more about the multiplexed method.>that can facilitate detection and differentiation of SARS-CoV-2 and influenza viruses
What does this sentence tell us?
The author is describing a new method, and the implications is that the mentioned attributes are what differentiate it from the previous method.
1. The multiplexed method can be used to detect influenza viruses. This implies that the previous method couldn't.
2. The multiplexed method can also be used to differentiate between COVID and influenza. This implies that the previous method couldn't.
Multiplexed means detecting two or more signals, but does not necessarily imply being able to differentiate between the signals. The description of the method states that the multiplex method can not only detect a signal (as the previous COVID only assay), but tell the tester which signal they detected. The author specifically mentions the multiplex method can detect influenza viruses, contrasting with the previous method, which is implied to not be able to detect them. If it can't detect the signal in the first place, differentiation is not something that would happen. You are interpreting this sentence as meaning that the previous method could identify influenza, but not differentiate it. This is not correct, it reads that the new test can both detect influenza and COVID at the same time, and then let the tester know which one, if not both, they detected in the sample. The old test could only detect COVID, meaning no differentiation ever happened.