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Should I put an auxiliary verb ('is') in this case?

I've never understood what is the difference between subject A and B.

or it should be

I've never understood what the difference between subject A and B.

(omitting the auxiliary verb 'is') Somehow the latter choice looks more natural to me but I'm not sure.

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    No: Your first example is fine, but the second is ungrammatical without "is". Note that you can insert "is" at the end of the clause ("I've never understood what the difference between subject A and B is) and both examples would then be fine and interchangable.
    – BillJ
    Apr 9 at 6:53
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    Or "what the difference is..." Apr 9 at 7:52
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    In my experience the first sentence, although grammatical, is slightly unusual and perhaps slightly unidiomatic, at least in BrE. The second sentence is obviously wrong (although it would work fine if the word "what" were omitted entirely). I agree with Kate Bunting that "is" can go after the word "difference". It can also go right at the end, although this might work less well if "subject A and B" were a long phrase.
    – rjpond
    Apr 9 at 8:02
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    If you include is as per your first example, strictly speaking you're "ungrammatically" embedding a question into your assertion - same as, for example, I don't know what is your name (which should more properly be phrased as I don't know what your name is. BUT (particularly when elements "A" and "B" are relatively long noun phrases) that little "copula" seems a bit forlorn when tacked onto the end of I've never understood what the difference between subject A and B is. Apr 9 at 12:21
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    Does this answer your question? "Do you know where's Linda?" vs "Do you know where Linda is?" Apr 9 at 12:23
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In a direct question we ask What is it? or What is the difference? or What is the difference between A and B?

But when we change it back to an indirect question we rarely keep the verb in the same position. Instead we say things like I asked him what it was or I wonder what it is or I don't know what it is.

I don't know what is it is grammatically defensible but sounds like something a non-native speaker would say. I would only say it this way if it was two separate sentences ("I don't know - what is it?"). Perhaps with a noun rather than a pronoun it is less unidiomatic but it is still an unusual wording (I don't know what is the difference) - we might use it if we were emphasising the word "what".

We would normally say either I've never understood what the difference is between A and B or I've never understood what the difference between A and B is.

You can also miss out both "what" and the copula, and say "I've never understood the difference between A and B".

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[1] I've never understood [what is the difference between subject A and B].

[2] I've never understood [what the difference between subject A and B is].

The simple answer to your question is no. The bracketed clause requires a verb, either after the subject "what", as in [1] or at the end of the clause as in [2].

The clause in question is an interrogative subordinate clause (embedded question) functioning as complement of "understood".

The meaning is:

"I've never understood the answer to the question 'What is the difference between subject A and B?'"

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  • What is your objection, if any, to [3] I've never understood [what the difference is between subject A and B]?
    – rjpond
    Apr 9 at 8:59
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I've never understood what is the difference between subject A and B.

I've never understood what the difference between subject A and B.

Neither example is satisfactory. You could write:

I've never understood what the difference between subject A and B [is].

'what the difference between subject A and B is' is the direct object of the verb 'understood'.

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  • There's nothing wrong with the first example. As an alternant it can also occur at the end of the clause, as you suggest. The clause is not a direct object but a subordinate interrogative clause (embedded question) functioning as complement of "understood".
    – BillJ
    Apr 9 at 6:58

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