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The letter appeared to be from Osama bin Laden's deputy Ayman al-Zawahiri to Abu Musab al-Zarqawi, said Pentagon spokesman Bryan Whitman.
He did not show the letter or say how or where it was obtained, but said it was considered authentic and recent.
The missive warned that the network faced crises in many areas, he said."Zawahiri says that they've lost many of their key leaders and that they've virtually resigned themselves to defeat in Afghanistan, that their lines of communication and funding have been severely disrupted," Mr Whitman told reporters on Thursday.