computers wouldn't work if data was automatically recovered or left intact after a delete or format. once it's flagged as empty in the file system, it's as good as 0'd out unless you are trying to hide something from someone who knows how to reconstruct deleted files.
it's possible to have a boot sector virus still on there after rebuilding a specific partition, but any decent bios for the past 15 years restricts access to the boot sector so that shouldn't be the case. if there appeared to be residual stuff on a drive after a fdisk/format/install, then almost certainly another partition or some of the backed up data had the virus in there. or, some viruses hop across a network very easily, reinfecting a computer once it's back up and on the network.