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The earliest coronavirus strains circulating in Italy did not come directly from China, according to a new study.

Researchers in Milan collected more than 300 blood samples of Covid-19 patients from the Lombardy region between February and April and traced the origin of the viral strains by changes in their genes.

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Italy was the first country in the world that put up a travel restriction barring all flights from China, but the genome sequencing suggested “a transmission chain not directly involving China”, said the researchers led by Professor Carlo Federico Perno of Milan University in a non-peer-reviewed paper posted on medRxiv.org on Monday.

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Lombardy had the earliest known outbreak in the West and has accounted for more than a third of the coronavirus cases in Italy. It is Italy’s richest region with thriving businesses, international transport connections and densely populated urban areas.

Sars-CoV-2, the virus that causes the disease Covid-19, was isolated and sequenced by Chinese researchers in early January. It was not until February 20 that the first case of local infection was confirmed by Lombardy’s health authorities, but “sustained community transmission was ongoing way before” that date, the researchers said.

Perno’s team collected blood samples from 371 patients in 12 provinces across the region. They were randomly chosen from people admitted to hospital with mild, moderate or severe symptoms. About 7 per cent of the samples failed to produce high-quality reading of the virus’ full genome, but the remainder still provided the largest sample base so far from the Lombardy region.

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The strains belonged to two separate lineages, each playing a dominant role in some provinces. But they “did not contain viral strains isolated in the first months of the outbreak in China”, said the paper.

Italy banned travellers from China on January 31, after a Chinese couple tested positive for Covid-19 in Rome. But according to a study by the Italian National Institute of Health last month, the virus had already appeared in sewage water in Milan and Turin in mid-December.

Perno’s new study showed that there could have been “multiple introductions” of the virus to the Lombardy region. These strains formed relatively isolated clusters in separate areas. One possible direction of the source was Central Europe, where strains with similar mutations had been detected, according to the researchers.

Their calculation suggested that these entries may have happened in the second half of January, based on the assumption that the virus was mutating at a relatively constant speed – although that may not have been the case.

The Italian study is one of several around the world to have found strains that were not traced to China.

In New York, the viral strains circulating in March did not come from China, which researchers said “was unanticipated” because government scientists had gone put extra emphasis on collecting samples in Chinese-speaking neighbourhoods.

“Rather, the sequence analysis suggests probable introductions of Sars-CoV-2 from Europe, from other US locations and local introductions from within New York,” said the official report of the joint research by the city’s Department of Health and the US Centres for Disease Control and Prevention, released last Friday.

A study by the Pasteur Institute in Paris in May confirmed that the outbreak in France had no direct link to China. Another study by Russian government scientists identified 67 introductions into their country and found only one that related to a Chinese source.

Some other studies challenged the belief that the pandemic originated in Wuhan, where the virus was first detected in late December.

A research team led by Spain’s top biologists identified the virus in a waste water sample in Barcelona dated back to March last year. In the Brazilian beach town Florianopolis, drainage samples collected and stored in government research facilities in November later tested positive for the coronavirus.

Benjamin Neuman, professor and chair of biological sciences with the Texas A&M University Texarkana, said that the recent findings could be “potentially a really big story” but that the data would require more scrutiny.

For example, the viral strains detected in sewage samples should have their genome sequenced to determine their position in the evolutionary tree, he said.

“If the sequences are indeed from that early part of the outbreak, it should resemble the earliest sequences from China, possibly with mutations that have not yet been seen,” Professor Neuman said.

They “should not have some of the mutations that appeared later in other parts of the world
”, he added.

A government epidemiologist in Beijing, who asked not to be named because they were not authorised to speak to the media, said tracing the origin of the coronavirus by its genes had limitations.

The copies preserved in poor environments such as waste water were probably compromised and unlikely to produce full genome sequences, they said. It would be difficult to estimate a strain’s “age” by mutation because a genetic change appearing later in an international database may not mean it was younger than those sequenced earlier.

“A mutation could be in circulation for some time in a remote corner of the world,” said the researcher. “Can we say that it did not exist until sequencing?”

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