“We identified 229 intra-host variants at 182 sites … [They are] reflecting highly dynamic intra-host viral populations,” said the team led by professor Li Mingkun of the Beijing Institute of Genomics at the Chinese Academy of Sciences in a peer-reviewed paper published in the Journal of Genetics and Genomics on Sunday.

These mutations were mostly detected in a single strain of the virus isolated from a single person. Some scientists suspected they could be the tip of the iceberg because most of the populations were not sampled. The virus could also mutate to different strains inside the same host, a phenomenon known as intra-host mutation.

But the scientists had no solid proof. Although some varying strains had been isolated from the same patient, they could be the result of co-infection.

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The evidence was contained in stool samples, according to Li’s team. They collected faecal samples from nine children who were recovering from the disease at the Guangzhou Women and Children’s Medical Centre in China’s southern Guangdong province.

Compared to oral or nasal swabs, a stool sample contained more viral material, Li and his colleagues found. This is likely because, according to some previous studies, the coronavirus could efficiently invade cells on the surface of human intestines.

Viruses mutate all the time and most changes in the new coronavirus genes do not appear to have any consequences. But in one child, the researchers found an unexpected mutation from samples taken just one day apart. The mutation could modify proteins, causing changes to the virus’ physical structure and activities, although the exact effects are yet to be investigated.

Similar genetic changes also happened to other children within a relatively short interval of five days, according to the study.

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Li said the study he led revealed some alarming signs. The rapid changes in the viral genes appeared to be a defensive response to the antiviral drugs used on these young patients. And the frequency of genetic changes varied from one child to another. These changes followed a random rather than coherent pattern.

These issues would make tracking and predicting the virus’ future mutations more difficult, according to the researchers.

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A Shanghai-based government biologist studying the coronavirus’ response to the human immune system said intra-host mutation could be an important problem hindering our understanding of the coronavirus, but the new study had not answered all the questions.

For instance, it remained uncertain whether the viral strains isolated from the stool samples were still active. For safety concerns, the samples were heated before analysis.

“For more solid proof, they will need a larger sample size,” said the researcher who was not involved in the study but asked not to be named because she needed official authorisation to speak to the media on Covid-19-related issues.

The stability of the virus is good news for drug and vaccine developers, whose products are mostly designed based on the first strains reported in the early stage of the pandemic. But some studies also suggested that co-infection with different strains of the coronavirus could make symptoms worse, and in most countries there was no measure to deal with the co-circulation of mutated strains in the upcoming winter.

“Our study highlighted the need for extensive studies on the intra-host variant dynamics … spanning a wide range of ages, disease severity and geographic regions,” said Li and his colleagues.