Chinese Covid-19 strains, study released - mutations -- [gilmay97 at gmail.com: South China Morning Post]

[Zenaan Harkness]

This an interesting virus, 'at's fer surely!


----- Forwarded message from Gil May <gilmay97 at gmail.com> -----

From: Gil May <gilmay97 at gmail.com>
Date: Thu, 30 Apr 2020 15:11:39 +1000
Subject: South China Morning Post

*Coronavirus’s* ability to mutate has been vastly underestimated, and
mutations affect deadliness of strains, Chinese study finds

By Stephen Chen

April 21, 2020

A team led by Professor Li Lanjuan has studied how the novel coronavirus
mutates and possible implications for the pandemic. Photo: EPA-EFE

A new study by one of China’s top scientists has found the ability of the
new coronavirus <https://www.scmp.com/coronavirus> to mutate has been
vastly underestimated and different strains may account for different
impacts of the disease in various parts of the world.

Professor Li Lanjuan and her colleagues from Zhejiang University found
within a small pool of patients many mutations not previously reported.
These mutations included changes so rare that scientists had never
considered they might occur.

They also confirmed for the first time with laboratory evidence that certain
mutations could create strains deadlier
<https://www.scmp.com/news/china/science/article/3079879/chinas-initial-coronavirus-outbreak-wuhan-spread-twice-fast-we>
than
others.

“Sars-CoV-2 has acquired mutations capable of substantially changing its
pathogenicity,” Li and her collaborators wrote in a non-peer reviewed paper
released on preprint service medRxiv.org on Sunday.

Li’s study provided the first hard evidence that mutation could affect how
severely the virus caused disease or damage in its host.

Li took an unusual approach to investigate the virus mutation. She analysed
the viral strains isolated from 11 randomly chosen Covid-19 patients from
Hangzhou in the eastern province of Zhejiang, and then tested how
efficiently they could infect and kill cells.

The deadliest mutations in the Zhejiang patients had also been found in
most patients across Europe, while the milder strains were the predominant
varieties found in parts of the United States, such as Washington state,
according to their paper.

A separate study had found that New York strains had been imported from
Europe. The death rate in New York was similar to that in many European
countries, if not worse.

But the weaker mutation did not mean a lower risk for everybody, according
to Li’s study. In Zhejiang, two patients in their 30s and 50s who
contracted the weaker strain became severely ill. Although both survived in
the end, the elder patient needed treatment in an intensive care unit.

This finding could shed light on differences in regional mortality. The
pandemic’s infection and death rates vary from one country to another, and
many explanations have been proposed.

Genetic scientists had noticed that the dominant strains in different
geographic regions were inherently different. Some researchers suspected
the varying mortality rates could, in part, be caused by mutations but they
had no direct proof.

The issue was further complicated because survival rates depended on many
factors, such as age, underlying health conditions or even blood type.

In hospitals, Covid-19 has been treated as one disease and patients have
received the same treatment regardless of the strain they have. Li and her
colleagues suggested that defining mutations in a region might determine
actions to fight the virus.

“Drug and vaccine development, while urgent, need to take the impact of
these accumulating mutations … into account to avoid potential pitfalls,”
they said.

Li was the first scientist to propose the Wuhan lockdown,
<https://www.scmp.com/news/china/society/article/3078189/build-coronavirus-lockdown-inside-chinas-decision-close-wuhan>
according
to state media reports. The government followed her advice and in late
January, the city of more than 11 million residents was shut down overnight.

The sample size in this most recent study was remarkably small. Other
studies tracking the virus mutation usually involved hundreds, or even
thousands, of strains.

Li’s team detected more than 30 mutations. Among them 19 mutations – or
about 60 per cent – were new.

They found some of these mutations could lead to functional changes in the
virus’ spike protein, a unique structure over the viral envelope enabling
the coronavirus to bind with human cells. Computer simulation predicted
that these mutations would increase its infectivity.

To verify the theory, Li and colleagues infected cells with strains
carrying different mutations. The most aggressive strains could generate
270 times as much viral load as the weakest type. These strains also killed
the cells the fastest.

It was an unexpected result from fewer than a dozen patients, “indicating
that the true diversity of the viral strains is still largely
underappreciated,” Li wrote in the paper.

Professor Li Lanjuan is a leading Chinese epidemiologist. Photo: Xinhua

The mutations were genes different from the earliest strain isolated in
Wuhan, where the virus was first detected in late December last year.

The coronavirus changes at an average speed of about one mutation per
month. By Monday, more than 10,000 strains had been sequenced by scientists
around the globe, containing more than 4,300 mutations, according to the
China National Centre for Bioinformation.

Most of these samples, though, were sequenced by a standard approach that
could generate a result quickly. The genes were read just once, for
instance, and there was room for mistakes.

Li’s team used a more sophisticated method known as ultra-deep sequencing.
Each building block of the virus genome was read more than 100 times,
allowing the researchers to see changes that could have been overlooked by
the conventional approach.

The researchers also found three consecutive changes – known as
tri-nucleotide mutations – in a 60-year-old patient, which was a rare
event. Usually the genes mutated at one site at a time. This patient spent
more than 50 days in hospital, much longer than other Covid-19 patients,
and even his faeces were infectious with living viral strains.

“Investigating the functional impact of this tri-nucleotide mutation would
be highly interesting,” Li and colleagues said in the paper.

Professor Zhang Xuegong, head of the bioinformatics division at the
National Laboratory for Information Science and Technology at Tsinghua
University,
said ultra-deep sequencing could be an effective strategy to track the
virus’ mutation.

“It can produce some useful information,” he said.

But this approach could be much more time consuming and costly. It was
unlikely to be applied to all samples.

“Our understanding of the virus remains quite shallow,” Zhang said.
Questions such as where the virus came from, why it could kill some healthy
young people while generating no detectable symptoms in many others still
left scientists scratching their heads.

“If there is a discovery that overturns the prevailing perception, don’t be
surprised.”



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