PHP文件流和病毒

I'm designing a website for my university's engineering related program. I've just added file uploads for registered users to host projects files they are working on. These uploads are done using a html form. The form and file data is passed to the server using Ajax which then uploads the file to Amazon web services s3. The file is not stored locally. Links are then provided on the user's page. The user base is small for know but I'm worried with more users there will be a risk of virus uploads. Could infected files uploaded with this method be executed on the server? Also is there an alternate way of accomplishing this or preventing virus uploads?