Ozone, a special form of oxygen that screens out harmful ultraviolet rays, reaches high concentrations twelve miles above Earth, where it has long appeared that it was immune from human influence; we have now realized, though, that emissions of industrial chlorofluorocarbons deplete the ozone layer.
has long appeared that it was immune from
has long appeared to have been immune from
has long appeared as being immune to
had long appeared immune to
had long appeared that it was immune to
You don't need an actual past-tense verb. You just need a clear indicator of a definite point in the past——the point that serves as the point of view for "had ___ed".
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