The findings, published in PNAS, showed viruses were 10 times more successful if the infection started in the morning.
And the animal studies found that a disrupted body clock - caused by shift-work or jet lag - was always vulnerable to infection.
The researchers say the findings could lead to new ways of stopping pandemics.
Viruses - unlike bacteria or parasites - are completely dependent on hijacking the machinery inside cells in order to replicate.