Good antivirus software will typically scan the entire pendrive when you insert it onto your computer, or when you access files on the pendrive. You can install antivirus software on your own computer, so that if you plug the USB pendrive into your own computer, your own computer won't be infected by the virus on the pendrive. You can't protect the USB pendrive by installing software on it. If the lab's machines are infected, there's not really anything you can do to protect yourself.
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