This small study found that thermal inactivation adversely affected the results of later RT-PCR tests, and suggests that other methods may be necessary. 

Nucleic acid testing (NAT) has played an important role in patient diagnosis and management of COVID-19. Some have recommended thermal inactivation at 56 °C to inactivate the virus before NAT. This could theoretically disrupt nucleic acid integrity virus and cause false negatives in RT-PCR tests.

Researchers examined if this was true. They found that Ct values were increased in specimens from diagnosed COVID-19 patients in RT-PCR tests after thermal incubation. About 50% of the weak-positive samples were RT-PCR negative after heat inactivation in at least one parallel testing. The use of guanidinium-based chemical lysis for preservation of these specimens had a smaller impact on RT-PCR results, with fewer false negatives (13.3%) and significantly less increase in Ct values than heat inactivation.