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She looks as if she has been ill.

vs.

She looks as if she had been ill.

What is the difference in the meaning between these two sentences?

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To me, the second sentence seems unnatural. The pluperfect ("had been") describes past actions occurring before other past actions. The sentence doesn't have another past action, so I don't see the function of the pluperfect in that case. I think it would be better to say

She looked as if she had been ill...

where the timeline is more clearly defined.

Now, to the first sentence:

She looks as if she has been ill.

To me, this suggests one of two things:

  1. She was ill, but recently got better.
  2. She is still ill.
1

To put it simply, the difference is present vs. past.

Present: She looks as if she has been ill.

Past: She looked as if she had been ill.

Has and Had is used exactly the same with the difference being, respectively, one is used with present tense and when discussing present events/conditions, and the other is used with past tense and when discussing topics in the past.

Specifically,

Has is used when length of the described event started in the past and ended / continuing in the present.

Had is used when length of the described event started in point A. in the past and ended in point B. in the past. Consequently, using it in the sentence "She looks as if she had been ill" is illogical and therefore is incorrect grammar-wise.

https://www.merriam-webster.com/dictionary/has

https://www.merriam-webster.com/dictionary/had

http://www.differencebetween.net/language/difference-between-has-and-had/

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Different dialects of English use "Ill" to mean different things: some use to mean "not feeling well", others use it to mean "to vomit".

Given that I'd expect to see people use the pluperfect "had been ill" for vomiting. It's an action which has been completed in the past and something else has happened since. For example if they see her coming back from the bathroom with water on their face, meaning she'd gone to the bathroom to vomit, but now is able to have another beer.

Whereas I'd expect people to use the perfect "has been ill" to to indicate that someone looked like they'd recovered from an illness some indefinite time ago.

However a speaker might, for emphasis, want to use the pluperfect to indicate that the person had very definitely finished being unwell. For example a cancer patient who has been cured may not have grown their hair back, but has recovered all their physical strength. Here the pluperfect is being used to add emphasis to the fact the illness has finished in the past.

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  1. She looks as if she has been ill.

It means it is very possible that she has been ill.

  1. She looks as if she had been ill.

This is wrong.

  1. She looked as if she had been ill.

It means, in fact, she hadn’t been ill.

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