This variant of covid is very deadly. able to evade standard tests, detectable only deep in the lungs

[The_King]

A variant of the coronavirus that caused a deadly outbreak in France can evade standard tests, detectable only deep in the lungs, according to a new study.

In a paper published on the preprint service medRxiv.org on Monday, researchers in western France said that only 15 per cent of patients in their study who had the B.1.616 variant tested positive in standard nasopharyngeal swabs, versus the 97 per cent hit rate for other variants circulating in France.

And nearly half of the patients died in less than a month, a much higher rate than the 16 per cent mortality among other hospitalised Covid-19 patients.

“[The] new variant [is] poorly detected ... with high lethality,” the researchers led by Pierre Fillatre, from the Centre Hospitalier de Saint-Brieuc, said in the paper. The study has not been peer reviewed.

Covid-19: coronavirus variants seen in Britain, South Africa spread worldwide

 

An infectious disease researcher with the Institute of Microbiology under the Chinese Academy of Sciences in Beijing said the variant, first detected in France earlier this year, had made the Chinese health authorities “quite nervous”.

 

 

With large-scale testing and contact tracing, China has been able to quickly suppress nearly all outbreaks at home for more than a year. The central government requires all Chinese cities, including those with more than 10 million residents, to be able to roll out blanket testing programmes within a week after an initial case is reported.

 

“If the mutation escapes surveillance, the whole system will collapse,” the Beijing-based researcher said, asking not to be named due to the sensitivity of the issue.

 

In early January, the Lannion hospital in Cotes-d’Armor had an unexpected outbreak of an infectious disease, the paper said. The patients had the typical symptoms of Covid-19, but most of their standard RT-PCR swab tests came back negative.

 

 

Doctors were puzzled because these patients were admitted for non-Covid-19 reasons, tested negative before admission, and stayed in wards strictly separated from Covid-19 patients.

 

From deep inside their lungs, researchers isolated an unknown variant of the Sars-CoV-2, the virus that causes Covid-19.

 

The B.1.616 variant in the patients has nine mutations across its genome, including one known as E484K at the spike protein. The mutation is also present in two variants of concern from South Africa and Brazil and can allow the virus to bypass immune protections formed with previous infections or vaccination, according to Fillatre and colleagues.

 

The variant might have dodged the conventional testing by reducing infection at the upper respiratory tract, the researchers speculated.

 

Some viral particles might still linger at the nose or throat, but their number could be “below the limit of detection” by commercial testing kits, they said.

The French researchers were surprised by the variant’s high fatality rate – it killed 44 per cent of its victims, or nearly three times the rate of the 

B.1.1.7 variant first detected in Britain

 

But the French variant has one weakness. The researchers compared its spread to other variants such as B.1.1.7, and found that the outbreaks were limited mostly to small clusters.

 

This could be a result of less viral shedding from coughing or sneezing.

 

To avoid being detected, the virus might have sacrificed some of its transmission potential, and thus lost an edge in competition with other variants prevailing in local communities such as the British strain, the researchers said.

The World Health Organization has classified the French variant as a “variant under investigation” and called for more studies to assess its threats.

 

The good news is that none of the variant’s mutations occurred in the genes targeted by testing kits, so there is still a good chance the virus can be detected if samples are taken deeper in the lungs, according to the French researchers.

They also said the high death rates should also be treated with caution because most of the patients who died in their hospitals were around 80 years old.

[XianGe]

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