Here is the full list of all 13 A Virus Named TOM trophies - there are 9 bronze, 3 silver and 1 gold.
Infect all levels, leaving none skipped
Earn GOLD for all Levels
Beat Level 6.10 Without Dying
Beat Level 3.04 WITHOUT Stealing Energy
Get a Energy Chain of 20 Energy Pellets
Get an Energy Chain of 10 Energy Pellets
Beat Level 3.10 WITHOUT Dropping Any Glitches
Beat Level 4.05 WITHOUT Stealing Energy
Collect more energy than the HUD capsules can contain
Beat Level 6.05 WITHOUT Stealing Energy
Complete City of Tomorrow
Score higher than the Devs on any Single Player level 3.01 or higher ("Tim" and "Jeremy" BAKED IN Scores)
Get TWO Energy Pellets Orbiting TOM at the Same Time