Slight modification, if you want to minimize the impact on Amazon’s original setup:
sudo pip install --upgrade pip
sudo cp /usr/local/bin/pip2.7 /usr/bin/pip-2.7
sudo ln /etc/alternatives/pip /usr/bin/pip
sudo rm /usr/local/bin/pip
sudo pip install --upgrade virtualenv
sudo cp /usr/local/bin/virtualenv /usr/bin/virtualenv-2.7
sudo ln /etc/alternatives/virtualenv /usr/bin/virtualenv
sudo rm /usr/local/bin/virtualenv
Manually installing pip deletes the /usr/bin version and puts it under /usr/local/bin, even on an upgrade, so you have to fix that up manually. I’m not entirely sure what will happen if Amazon ever bothers to update it, but this definitely needs to be part of the Amazon-specific script.
If you don’t set the links back up, then it needs
hash -r to run pip at all, and stops working with sudo.
Once done, LE works like a charm again.