"They've been hit hard in a few cases, but they definitely are involved in the fight — absolutely," said Seth G. Jones, a senior political scientist at RAND Corp.
Jones, a former adviser to the commander of U.S. special operations forces in Afghanistan, recently returned from a trip to eastern Afghanistan where he learned that al-Qaida's support network has expanded and its relations with groups such as the Pakistani-based Haqqani network are strong.
"That's a very serious concern because that kind of environment would allow al-Qaida to continue to operate, at least at a small level, because it's a workable environment for them, he said.
Richard Barrett, head of a U.N. group that monitors the threat posed by al-Qaida and the Taliban, said al-Qaida fears the Taliban will strike a deal with the Afghan government that would make the group all but irrelevant.
"So they will be doing whatever they can to assert their influence, to assert their presence" in Afghanistan, he said.
At least for now, al-Qaida in Afghanistan has no capability to launch attacks on the U.S., although commanders are taking no chances.
Little-noticed fragmentary U.S. military accounts of raids and strikes against al-Qaida in the northeastern provinces of Kunar and Nuristan show the group retains a command structure inside Afghanistan. On May 27 the U.S. killed the No. 2 commander in Afghanistan, Saudi national Sakhr al-Taifi, in Kunar, but it has yet to catch up to the top al-Qaida commander in the country, identified by U.S. officials as Farouk al-Qahtani, who resides in Nuristan.
In early September the international military coalition announced the death of an al-Qaida operative, Abu Saif, described as an associate of an al-Qaida leader killed along with several of his fighters July 1 in Kunar. Saif was called a conduit between senior al-Qaida leaders in Pakistan and Afghanistan, passing messages between them. In the most recent strike, officials said Sept. 27 they killed al-Qaida "facilitator" Abdul Rauf in Kunar. He was a Pakistani coordinator of foreign fighters' movements into Afghanistan and a builder of improvised explosive devices for attacks on coalition troops.
Interviews with Afghan officials suggest that al-Qaida also is present in other parts of the country, including the northwestern province of Faryab as well as Logar province, just south of Kabul.
Logar's provincial chief of police, Gen. Ghulam Sakhi Roogh Lawanay, said it is difficult to know how many militants are directly affiliated with al-Qaida, but he estimated their numbers in Logar at 100 to 150.
"Al-Qaida is very active. It is like fish. When one fish dies, another comes," he said in a recent interview. "The determination of these Arab fighters is high."
In interviews in Kabul and Washington, U.S. officials said they are satisfied that al-Qaida is so small inside Afghanistan — they put the number at between 50 and 100 fighters — that they can be contained indefinitely if the Afghan government allows U.S. counterterrorism forces to monitor and hunt the remnants. U.S. and Afghan officials are working to craft talks on a bilateral security agreement that could include such an arrangement.
Al-Qaida's numbers, however, don't tell the whole story.
Allen has said al-Qaida has learned to leverage its presence in Afghanistan to give the impression of having withstood U.S. military might and to burnish its image as a global force.
U.S. commanders say they will keep up pressure on al-Qaida to frustrate its goals, but few believe al-Qaida will be gone before U.S. troops leave.
"I see no evidence to suggest that it will be eliminated by 2014," said Jones, the RAND analyst.
Associated Press writer Amir Shah contributed to this report.
Robert Burns can be followed on Twitter at http://www.twitter.com/robertburnsAP
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