(Other posts on SO are similar, but none have the specific combination of uwsgi + Flask + virtualenv) (This one is closest)
I installed uwsgi via apt-get. I also tried
See the answer from @JRajan first.
If you're sure you just want to suppress the error and not actually solve the underlying issue, you should add --no-site to your command or no-site=true to your uwsgi.ini file.
--no-site
no-site=true