Lack of sleep and stress can also manifest as flu-like symptoms for me. Finding a working sleep-wake rhythm has been really difficult since working at home full-time. I love the freedom of fully being able to schedule my work hours, but it also means that I now have full control and responsibility over the rest of my daily schedule, and maintaining a healthy schedule takes more effort than I'd have expected.
What really helped me is to go out and exercise in the morning, rather than lounge inside until I start work. I have more clarity during the day, which means I feel less compelled to work late to make up for my self-perceived lack of focus during the work day. And less work in the evening also means I fall asleep more easily, which has really been an issue for me in the past few months.
YMMV, of course.