The two pieces of evidence from the text that best support the inference that honeybees—not bumblebees—are responsible for infecting the studied flowers are:
C. All the infected flowers researchers picked and tested were close to apiaries.
D. All of the honeybees researchers collected were infected with both viruses.
These answers indicate a direct connection between honeybees and the infection of flowers, as flowers near apiaries (where honeybees are present) tested positive for the viruses, and all honeybees tested were infected.