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I have a medical device that is a USB client and has no internal power source/battery. It draws 5V from USB and also communicates to the Host via same interface. Device is intended to be used only with mobile android phones.

In this case, is the conducted emission test applicable? Since a mobile phone has only 1 USB port, there is no question of multiple devices being connected. (my understanding is that the conducted RF emissions test is not meant only to protect mains network like IEC 61000-3-2 harmonic current emission and IEC 61000-3-3 voltage fluctuations and flicker emission. So it should be applicable for any power or data ports that connect to external devices. Is this correct?)

If yes, how would the test setup be done? Since power and data lines are on the same USB interface, do I have to cut the cable and pass VBUS and GND through LISN and then connect data lines directly to phone?

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Yes I think it is, you need to test any normal operating modes and if you have a cable you should test it with that. I would talk to the NRTL that you are certifying with because it's going to be up to them how they want to test it. They may even say that you might have to certify with a PC.

I would think that they would only make you do radiated emissions since the device is not grounded

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