There are several causes leading to a perfusion defect on a VQ scan with an acute pulmonary embolus being only one of them:
Vascular causes
acute pulmonary embolus
previous pulmonary embolus (including fat embolism, thromboembolism, air embolism, tumor)
vasculitides affecting the pulmonary vessels
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granulomatous disease affecting vessels
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other conditions affecting vessels, e.g.
intravenous drug use (IVDU)
radiation therapy
pneumonectomy
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vascular compression/compromise from
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altered pulmonary circulation
cardiac disease
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