Htc desire 820s viruse!!!!

hi every one
my devices had some issue with sestem files
just manyunknown apps
i try factory reset/wipe data/dalvic cashe
but never delete any app from the phone
i download stock firmware to flash it via sp flashtool
but when i connect the phone via usb after press download(sp flashtool) no thing hapened
any solution for flash it
thx alot