There's no delicate way to put this: at least part of Apple's patent lawsuit against HTC appears to be a proxy fight for a larger issue with Android as a whole. Apple's complaint with the International Trade Commission makes an explicit distinction between HTC's Android devices and its WinMo phones (referred only to as "DSP Products"), and the Android sets are repeatedly called out for infringing certain patents. We don't know exactly what Apple's issue is yet -- the problem could be the specific way HTC implements Android, rather than Android itself -- but it's certainly a big shot across Google's bow. We'll keep reading and let you know what else we find out.
Update: We've gone through each of the patents in both lawsuits and we're more convinced than ever that this lawsuit is really about Android, not HTC. Check here for the full rundown.
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Apple / HTC ITC filing