Patient-derived mutations impact pathogenicity of SARS-CoV-2

[Treyfish]

Patient-derived mutations impact pathogenicity of SARS-CoV-2

Hangping Yao, Xiangyun Lu, Qiong Chen, Kaijin Xu, Yu Chen, Linfang Cheng, Fumin Liu, Zhigang Wu, Hai bo Wu, Changzhong Jin, Min Zheng, Nanping Wu, Chao Jiang, Lanjuan Li
doi: https://doi.org/10.1101/2020.04.14.20060160
This article is a preprint and has not been certified by peer review [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

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Abstract


The sudden outbreak of the severe acute respiratory syndrome-coronavirus (SARS-CoV-2) has spread globally with more than 1,300,000 patients diagnosed and a death toll of 70,000. Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with functional changes in viral pathogenicity.

Here we report functional characterizations of 11 patient-derived viral isolates, all of which have at least one mutation.
Importantly, these viral isolates show significant variation in cytopathic effects and viral load, up to 270-fold differences, when infecting Vero-E6 cells. We observed intrapersonal variation and 6 different mutations in the spike glycoprotein (S protein), including 2 different SNVs that led to the same missense mutation. Therefore, we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity.
..https://www.medrxiv.org/content/10.1....14.20060160v1

[Treyfish]

Published: 10:41pm, 20 Apr, 2020

• A team led by Professor Li Lanjuan has studied how the novel coronavirus mutates and possible implications for the pandemic
  Stephen Chen in Beijing
• The most aggressive strains of Sars-CoV-2 could generate 270 times as much viral load as the least potent type
• New York may have a deadlier strain imported from Europe, compared to less deadly viruses elsewhere in the United States

.
A new study by one of China’s top scientists has found the ability of
the new 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
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.

......

Li was the
first scientist to propose the Wuhan lockdown,
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.

...
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 uniqu........https://www.scmp.com/news/china/scie...-chinese-study

[Sally Furniss]

Thank you Treyfish ....The authors of the new Los Alamos study added that a higher level of infectiousness meant that if asymptomatic carriers accounted for a substantial proportion of transmission, then quarantine and tracing of contacts of those showing symptoms would not be enough to halt the virus’ spread.

“When 20 per cent of transmission is driven by unidentified infected persons, high levels of social distancing efforts will be needed to contain the virus,” they said.

...more https://www.scmp.com/news/china/scie...-twice-fast-we

[JJackson]

If a mutation provides a selective advantage then it will start to dominate and displace less fit strains. There is no evidence that this is occurring. Each branch in the phylogenic tree is holding its own against the other branches. This may change at some point but is not happening at the moment based on the existing sequence data.
While this does not preclude differences in virulence I have not seen anything reported that would imply there is any noticeable difference in strain virulence in different areas.
The tree below shows the EU and US sequences and they are both to be found across the whole tree

[Treyfish]

BIOLOGICAL NEWS

Watching For Mutations in the Coronavirus


By Derek Lowe 21 April, 2020

The coronavirus outbreak has been accompanied by a huge amount of sequencing data, as well it should be. Nextstrain.org is a great place to see this in action: region by region, the spread of the infection can be tracked, often with enough detail to say where the virus must have come in from and how many different starting points it’s had. That all depends on how many different strains are detected in the first place, of course, and in regions (like the US!) where we’re not even doing enough basic RT-PCR swab tests to know the prevalence of the virus as a whole, we’re surely missing a lot of information about deeper thinks like viral sequence, the number of different mutations, and how they’re distributed. GISAID is another large repository of such data, and it’s growing day by day.

As you can see from these sites, there are a lot of random single-nucleotide changes that have popped up. It’s important to realize that overall, the mutation rate of this virus is not particularly high (in line with other coronaviruses, actually). But they do accumulate; there’s a fearful amount of viral replication going on out there, and not all of it goes perfectly. A single patient may have several mutational strains going at the same time as the virus replicates, and there’s been a report of a person who turned out to be infected simultaneously by two strains with different geographic origins, which is bad luck. Take a look at the Nextstrain diversity panel here to get an idea of what’s been found across the sequence (reproduced below). These are total events, the number of times mutations have been seen, and remember, because of the triplet genetic code, some of these single-nucleotide variations are still going to lead to the same amino acid in the resulting proteins:



Here’s a general look at how that genome is organized. ORF (open reading frame) 1a/b the big orange bar and green bar in the graphic above) encodes nonstructural enzymes that are involved in replication (and in protein processing to enable that replication – this is the polyprotein mentioned this post). Then you get into some structural pieces: you have the S region which codes for the notorious Spike protein (the one that gives the virus its distinct appearance and that interacts with human ACE2 for cellular entry), ORF3a, a structural protein that is near the spike and likely modulates the human inflammation response (as it seems to in the earlier SARS coronavirus), the gene for the envelope protein (E), the membrane protein (M), the nucleocapsid protein (N), an RNA polymerase enzyme, and a few others. You can see above that there are known mutations scattered through the whole sequence, with some spots showing more than others. It’s worth comparing these in terms of entropy: how divergent are these mutations? Here’s that plot:



Note that the baseline goes down a lot; most of the mutations in the first count are trivial ones that don’t even change what amino acid gets coded for, or produce something quite similar. That second-biggest peak, for example, right at the end of ORF1a at the ORF1b border, doesn’t look so impressive when you see the entropy number and take into account what these mutations are coding....https://blogs.sciencemag.org/pipelin...he-coronavirus

[mscox]

Prior to the first 2019 genome sequences of sars-cov2, how many of its coding regions overlap or "perfectly" match with older (pre 2018) genbank (ie GISAID) sequences of other recorded virus genomes? What is the statistical likelihood that those coding regions would have remained "perfectly" unchanged (no random mutations) in the wild animal reservoirs prior to the theoretical zoonotic leap in Dec 2019?

Is that a leading question? Why, yes it is. But it is one that needs investigation and answering.

[JJackson]

MSCOX not clear about what you are asking here. The ORF1a/b is interesting in it that it uses a mechanism to cause it to occasionally 'slip' backwards at the a/b junction. The ORF1a reading frame normally reads all of ORF1, as the 1b start codon is out of sync. There is a NT sequence just after the 1b start codon that causes it to sometimes slip backwards a few NTs and read from the 1b start codon, which would normally be invisible (secondary reading frame). The RdRp protein, which is coded for towards the end of the the ORF1 polyprotein and cleaved into its biologically active form post translation, is heavily conserved across the range of corona viruses. It is obligatory for virion assembly. There has been a mutation found in Singapore with a 328NT deletion which removes almost all of ORF8 (a similar mutation was found in SARS-1) the virus was viable but I doubt it will persist for long against the wild types - time will tell.