Well trojan/viruses affects mostly executables so that they can harm the system. An infected jpg or video file is not harmful as such. But I have been a victim of a virus which swept my HDD of all the data along with partitions too

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Now for your issue...could you make a backup of all your data in some other portable HDD? Afterwards you can install your OS in fully formatted HDD.
Hey wait, there is one more way, although I would request others comments too...if you have any, install Linux on your machine. Download and install and antivirus and clean your HDD of all the viruses..