Peter Ben Embarek, who led a team of WHO investigators in Wuhan, said 13 different genetic sequences of the SARS-COV-2 virus were found in the Hubei province city, adding thousands more blood samples have been requested for analysis.
It suggests that the infection had been circulating in China earlier than previously thought, although Mr Embarek refused to be drawn on the matter.
Wuhan is widely considered to be "ground zero" of the outbreak, although its exact origins and timeframe continue to be debated, with some reports suggesting the disease was present in Europe as early as October.
In an interview with CNN published on Monday, Mr Embarek told the network "the virus was circulating widely in Wuhan in December, which is a new finding”.
Mr Embarek said Chinese officials had presented his team with 174 cases of coronavirus in and near the Wuhan area in December 2019, around 100 of which had been laboratory test-confirmed, with the remaining cases identified through the clinical diagnosis of the patients' symptoms.
He said this suggested there could have been as many as 1,000 cases of the disease in Wuhan by December. "We haven't done any modelling of that since," he said. "But we know... in big ballpark figures... out of the infected population, about 15 per cent end up severe cases, and the vast majority are mild cases."
Mr Embarek said that the 13 variants examined alongside other patient data across China in 2019 could provide vital clues to the origins of the outbreak.
He added: "Some of [the variants] are from the markets... some of them are not linked to the markets. This is something we found as part of our mission... part of the interaction we had all together."
Mr Embarek's comments came after a UK scientist on the Wuhan mission refused to rule out a lab leak as the possible source of the outbreak, contradicting an earlier finding.
Professor John Watson, a former deputy chief medical officer, said while China remained a “very, very possible source”, reports that the virus was circulating in other parts of the world, notably northern Italy, as early as September and October, warranted further investigation.
“I think that there are all sorts of reasons to do with the way it did start and the outbreak in Wuhan and the various bits of information about the way in which these viruses live in different animal reservoirs that suggest that China is a very, very possible source,” he told BBC One's The Andrew Marr Show.
But China was “by no means necessarily the place where the leap from animals to humans took place and I think we need to ensure that we are looking beyond the borders of China, as well as within China,” he added.
A study released by the National Cancer Institute (INT) in Milan in November showed the new coronavirus was circulating in Italy in September 2019.
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