Intelligence agencies and the N.S.C. produced early warnings.

National Security Council officials received the warnings in early January about the potential dangers from a new virus in Wuhan, China.

The State Department’s epidemiologist warned early that the virus could develop into a pandemic, while the National Center for Medical Intelligence, a small outpost of the Defense Intelligence Agency, reached the same conclusion. Weeks later, biodefense experts in the National Security Council office responsible for tracking pandemics looked at what was happening in Wuhan and started urging officials to think about what would be entailed in quarantining cities the size of Chicago and telling people to work at home.

But some of the earliest warnings came from national security hawks eager to blame China, and they often ran into opposition from the president’s economic advisers, who were concerned about upsetting relations with China at a time when Mr. Trump was negotiating a trade deal with Beijing.