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For a long time many scientists suspected that koalas were so lethargic because the compounds in eucalyptus leaves kept the cute little animals in a drugged­out state. But more recent research has shown that the leaves are simply so low in nutrients that koalas have almost no energy.

Can I use had suspected or had been suspecting instead of suspected? To me, it seems possible because "For a long time", the action of the verb was maintained for a certain duration of time.

Do the two of them have same meaning in the context above?

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All three are pretty much equal in meaning, but had suspected would be the preferred choice here, since it emphasises that this has now changed.

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