The correct option is A Air-quality indices rarely take long-term risk into account
In the given sentence, ‘they’ in the second clause seems to refer to ‘long-term risk’, which is the subject of the first clause. So it is grammatically incorrect.
Now let us look at the answer options.
Option C does not make sense. So we rule this out.
Option B has two independent clauses- (1) Rarely do air-quality indices take long-term risk into account, and (2) they also vary from place to place. Each of these is a sentence in its own right. When joining two independent clauses without the use of a coordinating conjunction (and, but, or, or nor), a semicolon has to be used, not a comma. So option B is incorrect.
In option A, again, there are two independent clauses - (1) Air-quality indices rarely take long-term risk into account, and (2) they also vary from place to place. The clauses are joined by a semicolon. So option A is grammatically correct.