COVID-19 Vaccine Update: Virus mutations in several children could complicate virus research

Stephen Chen in Beijing, South China Morning Post

According to a new study by Chinese scientists, the novel coronavirus is capable of rapid mutation in the gut of children.

As claims showed in estimates based on modeling, a Sars-CoV-2 viral strain accumulates typically one or two mutations per month as it spreads from one person to another.

But in the intestines of some children recovering from Covid-19, a “novel mutation” to change the virus’ form or function could occur within a day as they augmented inside the same carrier, the researchers discovered.

“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 advertised in the Journal of Genetics and Genomics on Sunday.

Mutations threaten the many drugs and vaccines under development to fight the pandemic. Scientists worldwide have classified more than 21,000 mutations that have occurred in the ribonucleic acid (RNA) of the Sars-CoV-2 virus so far, according to the China National Centre for Bioinformation.
These mutations were often detected in a single strain of the virus isolated from a single person. Some scientists suspected they could be the iceberg’s tip 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.

The scientists had no hard proof. Even though any different strains had been isolated from the same patient, they could result from co-infection.
The evidence was contained in stool samples, according to Li’s team. They collected fecal samples from nine children recovering from the Guangzhou Women and Children’s Medical Centre’s disease in China’s southern Guangdong province.

Li and his colleagues found a stool sample containing more viral material than oral or nasal swabs.

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 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’s physical structure and activities, although the exact effects are yet to be investigated.

As mentioned in the study, similar genetic changes also happened to other children within a relatively short interval of five days.

Is fast mutation terrible news? The research community had differing opinions.

Some scientists believed a mutation usually did more harm than good to the virus. But others were less optimistic because some viruses, such as HIV (human immunodeficiency virus), had used rapid mutation to dodge an attack by vaccine or drugs.

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 a coherent pattern.

As per information provided by the researchers, these issues would make tracking and predicting the virus’s future mutations more difficult.

A Shanghai-based government biologist studying the coronavirus’s response to the human immune system said intra-host mutation could be an actual problem hindering our understanding of the coronavirus. Still, 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 authorization to speak to the media on Covid-19-related issues.

An increasing number of scientists believe the novel coronavirus circulated quietly among humans for a long time before detection in December last year. Its structure was well-adapted to the human body and remained relatively stable, despite the large number of mutations recorded.

The virus’s stability 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. Although some studies also suggested that co-infection with different strains of the coronavirus could make symptoms worse. There was no measure in most countries to deal with the co-circulation of mutated strains in the upcoming winter.

Li and his colleagues stated that,

“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.”

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