Hi
It completely depend on the trojan/virus that you have, but yes certain can put themselves into the recovery partition, and other can destroy the partition altogether.
I suggest to do a clean install with a iso or media kit if you have one.
You can easily get an Windows 10 iso with the media creation tool from a working computer, and use that one. (https://www.microsoft.com/en-ca/software-download/windows10)
Thanks