How can I Isolate the Brotherhood virus?

I assume you mean this one? There is a detailed walkthru on that page.

The Courier must find the Virus on 3 terminals in 60 seconds to wipe it from the system. To do so, quickly enter each terminal and choose the only option you can. Then, if the text that shows up seems like a random string of letters and numbers, proceed to the next terminal. If you get a taunting message on the second screen, choose the option to isolate the virus. If you do not get all 3 terminals in the time limit, you will have to speak with Scribe Ibsen again. You will get a new 60 seconds and the terminals that the virus has infected will randomize.