I recently did a virus scan on my SD card on my PC, running Windows XP, and found few viruses. Will these viruses affect my mobile device running on Windows CE 5?
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It is highly unlikely, but also possible.
You do not list the virus in question, and without knowing this, it is impossible to say for sure.
Many malware programs on computers look to infect other machines by simply copying itself to everything they can, this includes all mass storage devices (USB & cards etc.), however, it is very likely it simply targets 32 and 64 bit operating systems.
Again, that being said, it isn't impossible for it to target handheld devices, but it is highly unlikely.
CE doesn't have the same "autorun" facility as XP, so it's highly unlikely that it would even attempt to launch.
If it did somehow attempt to launch, since the device is running on an ARM architecture processor, it is highly unlikely that the virus would have any ability to execute on the device.
If it did somehow execute, it's injection mechanism would likely be written, again, for X86 and/or using desktop exploits, which don't exist on CE, so it's highly unlikely that it would have any effect on the CE device.
Now if the virus were written specifically to target mobile devices, then it's a whole different story, but the ones you've mentioned were not.