I think the virus idea is perfect.
Doomsday fails because people keep trying to turn it into a character. Doomsday isn't a character, and never was. Doomsday is a plot device. A natural disaster. And making it a virus? After the last couple years does anyone need a run down on how that could be applied to countless stories?
* Clark Kent has to investigate rumors that a sample of the virus is being sold in a black market auction. Who's looking to buy? More importantly, who's looking to sell, how'd they get the sample, and what's Clark gonna do when he finds out?
* The new regime of the failed nation of Pokolistan (home of villains "Russian Zod," Ignition, etc.,) found a sample of the virus in the ruins of the once advanced country, and have used it to turn their military into a unique breed of super soldier. Clark must find out what Pokolistan's new rulers intend; world domination, or just safety and security for their people? Did they truly master this dangerous virus, or are those soldiers really just ticking time bombs?
* Superman crash lands on a planet where the entire sentient population was infected. Stranded with no friends, no resources, and no way off world, Clark has to find a way to survive a planet where every living thing is trying, and capable, of killing him. Give that planet a red sun if you really wanna get hardcore (I would).
* Once, in a moment of panic, Superman banished a Doomsday to the Phantom Zone, not considering that it adapts to any environment. Now the Fortress of Solitude is receiving a distress call from the Zone; Xa-Du is desperate. Why? What's happening in the Zone, is Clark really going to enter it to help some of his most devoted enemies? Or is it all just one of Xa-Du's tricks?
* Oh noes! Jimmy Olsen drank what he thought was a soda, but was in fact the Doomsday virus! Superman and special guest star Ray "Atom" Palmer must battle Doomsday....from *inside* Jimmy! Will our heroes purge the virus from Jimmy's bloodstream, or is Superman's Pal.....dare we say.....DOOMED?
If Doomsday is a virus, then you've got a threat on several levels. It can be a pure physical threat, someone the virus has completely infected and taken over, like presumably the original Doomsday was. Beyond the contagious phase but capable of murdering the hell out of Kryptonian level beings. Or it can fuel stories that have nothing to do with Doomsday the monster, it can just be a goal of the villain or a hazard for Clark to deal with. You can deal with a Doomsday and wrap up a story any way you like; kill it, banish it, whatever, and later bring in a new one without having to worry about continuity.
Doomsday as a virus is basically kryptonite that can punch back. You can basically do anything with it.