The discovery of how the variants were formed and then spread could help scientists to identify its source and explain why it is so contagious.
The researchers analysed the first 160 complete viral genomes sequenced from human patients between December 24 and March 4, then reconstructed the early evolutionary pathway of Covid-19 in humans through its mutations.
“There are too many rapid mutations to neatly trace a Covid-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously,” said Peter Forster, a geneticist at University of Cambridge and lead author of the study.
“These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is one of the first times they have been used to trace the infection routes of a coronavirus like Covid-19,” he said in a report about the study on the university’s website.
Type A was closest to the coronavirus discovered in bats and although found in Wuhan– the central China city that was the epicentre of the initial outbreak – was not the primary type there, they said.
Type A was also found in Americans who had lived in Wuhan, and in other patients diagnosed in the United States and Australia.
The most common variant found in Wuhan was type B, the study said, though this appeared not to have travelled much beyond East Asia before mutating, which the researchers said was probably due to some form of resistance to it outside that region.
Finally, type C was the variant found most often in Europe based on cases in France, Italy, Sweden and England. It had not been detected in any patients in mainland China, though had been found in samples from Singapore, Hong Kong and South Korea, the study said.
The researchers concluded that variant A was the root of the outbreak as it was most closely related to the virus found in bats and pangolins. Type B was derived from A, separated by two mutations, while type C was the “daughter” of variant B.
“The Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population,” Forster said.
“It may need to mutate to overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase.”
The research also documented how people’s movements had helped the spread of the virus.
For example, the study suggested that one of the earliest introductions of the virus to Italy – found in a Mexican traveller who was diagnosed on February 28 – came via the first documented German infection – a person who worked for a company in Munich – on January 27.
The German contracted the infection from a Chinese colleague in Shanghai, who had recently been visited by her parents from Wuhan.
The researchers documented 10 mutations in the viral journey from Wuhan to Mexico.
“Because we have reconstructed the "family tree" (the evolutionary history) of the human virus, we can use this tree to trace infection routes from one human to the next, and thus have a statistical tool to suppress future infection when the virus tries to return,” Forster said.
He added that researchers can better determine when the outbreak started with the data.
“I hope this improved knowledge of the origin and spread will enable more precise computer simulations to predict which measures will be most effective,” he said.
Lu Jiahai, an epidemiologist at Sun Yat-sen University Guangzhou, the capital of Guangdong, said the study had provided a preliminary analysis of genomics and molecular variation.
“The virus mutates during spreading and has become more adapted to transmission among humans in different populations from different countries,” he said.
But as the variants were related to each other, tracking mutations within different groups could help to determine the origin of the virus, he said.
“This research indicates that the spread of the virus is increasingly adapted to different populations and therefore the pandemic needs to be taken seriously,” Lu said.
“People need to pay more attention to prevention and control … the virus may coexist with humans for a long time.”
Guo Rui Guo Rui is a China reporter covering elite politics, domestic policies, environmental protection, civil society, and social movement. She is also a documentary filmmaker, recording modern Chinese history and social issues through film.
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