This glaring contradiction to GE for the influenza case has been recently discussed in the thread @Giltil initiated here:
Influenza may be in evolutionary stasis in its natural reservoir after all
But of course, the issue goes beyond just influenza and extends to all viruses everywhere, including coronavirus. Viruses by definition require the cellular machinery of mortal hosts to replicate, a process entirely exposed to GE; and yet through history until the present, they have been a persistent and pervasive presence. That we are supposed to accept that each and every pathogenic virus on the planet has been preserved and hiding out, biding their time as in some super villain’s lair, for thousands of years, is not just wrong but is outlandish.