Computers Uncover 100,000 Novel Viruses in Old Genetic Data (science.org) 50
sciencehabit writes: It took just one virus to cripple the world's economy and kill millions of people; yet virologists estimate that trillions of still-unknown viruses exist, many of which might be lethal or have the potential to spark the next pandemic. Now, they have a new -- and very long -- list of possible suspects to interrogate. By sifting through unprecedented amounts of existing genomic data, scientists have uncovered more than 100,000 novel viruses, including nine coronaviruses and more than 300 related to the hepatitis Delta virus, which can cause liver failure. "It's a foundational piece of work," says J. Rodney Brister, a bioinformatician at the National Center for Biotechnology Information's National Library of Medicine who was not involved in the new study. The work expands the number of known viruses that use RNA instead of DNA for their genes by an order of magnitude. It also "demonstrates our outrageous lack of knowledge about this group of organisms," says disease ecologist Peter Daszak, president of the EcoHealth Alliance, a nonprofit research group in New York City that is raising money to launch a global survey of viruses. The work will also help launch so-called petabyte genomics -- the analyses of previously unfathomable quantities of DNA and RNA data.
That wasn't exactly what computational biologist Artem Babaian had in mind when he was in between jobs in early 2020. Instead, he was simply curious about how many coronaviruses -- aside from the virus that had just launched the COVID-19 pandemic -- could be found in sequences in existing genomic databases. So, he and independent supercomputing expert Jeff Taylor scoured cloud-based genomic data that had been deposited to a global sequence database and uploaded by the U.S. National Institutes of Health. As of now, the database contains 16 petabytes of archived sequences, which come from genetic surveys of everything from fugu fish to farm soils to the insides of human guts. (A database with a digital photo of every person in the United States would take up about the same amount of space.) The genomes of viruses infecting different organisms in these samples are also captured by sequencing, but they usually go undetected.
That wasn't exactly what computational biologist Artem Babaian had in mind when he was in between jobs in early 2020. Instead, he was simply curious about how many coronaviruses -- aside from the virus that had just launched the COVID-19 pandemic -- could be found in sequences in existing genomic databases. So, he and independent supercomputing expert Jeff Taylor scoured cloud-based genomic data that had been deposited to a global sequence database and uploaded by the U.S. National Institutes of Health. As of now, the database contains 16 petabytes of archived sequences, which come from genetic surveys of everything from fugu fish to farm soils to the insides of human guts. (A database with a digital photo of every person in the United States would take up about the same amount of space.) The genomes of viruses infecting different organisms in these samples are also captured by sequencing, but they usually go undetected.
Photo size!? (Score:5, Insightful)
I know its not related to the main article, but I just wanted to call out a quick bullshit to this line, as a former semi-pro photographer.
"A database with a digital photo of every person in the United States would take up about the same amount of space."
If my math is serving me correctly, I'm over-estimating USA population at 350 million. And we're talking 16 petabytes of data? That would be roughly 61MB per photograph. WHAT THE HELL format are you using to require that much data? High quality/resolution RAW photos are ~30MB. Decent JPG images are ~1-3MB for the same resolution.
You're off quite a bit on your arbitrary comparison metric there!
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Fine. Whatever. Back to how many Volkswagen Beetles the photographs would all fit in. Is that precise enough for you?
raw files... (Score:1)
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Not sure your point here. RAW type formats are preferable for digital imaging (particularly if your going to be doing some deep analysis on them).
Its not about "Most people", its about "Most algorithms".
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Professional journalists copy/paste photos into Word documents so that their editor can open them, hence each one is about 60MB.
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Raw, uncompressed bitmaps of 20 megapixel images.
Doesn't everybody use those?
If that genetic material was old... (Score:5, Informative)
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It would be much more fun it if was, "Scientists accidentally unleash 100,000 previously unknown viruses". You would get people screaming it's the end of the world, other's screaming it's a conspiracy and insisting on drinking their own urine to "become immune", while the people focuses on the real issue will be screaming that the plural of "virus" is "virii". ;)
Re: If that genetic material was old... (Score:1)
Not if we don't try hard to port them to humans (Score:1, Troll)
Unless deliberate steps are taking to adapt these viruses to humans, there is no danger. Just wash your hands, and cook your meat thoroughly...
No, I'm not suggesting, COVID-19 virus was designed as a weapon or something like that. The charitable explanation [substack.com] is that it was adapted in order to study, how such an adaptation — should it ever happen naturally — can be treated.
And then it "escaped" — without our tr
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Unless deliberate steps are taking to adapt these viruses to humans, there is no danger. Just wash your hands, and cook your meat thoroughly...
There is another [deniskitchen.com] step you have to take...
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Yet again, a sober, well-informed comment - very likely close to the truth - gets moderated down.
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Yes, because it's against the CCP narrative and there are a bunch of wumaos here with sock puppet mod point accounts now that go through downvoting ALL posts from people who are critical of them.
As a result, ~25 years of Excellent Karma and even some recent article submissions getting posted mean nothing at all - I haven't seen any mod points in months.
Re: Not if we don't try hard to port them to human (Score:1)
Poor little wumao.
Make sure you don't spend your $0.50c all at once comrade !
Re:Not if we don't try hard to port them to humans (Score:5, Interesting)
I know the linked PREEMPT study *sounds* nefarious -- inserting novel spike protein into SARS-COV-1 viruses -- but if SARS-COV-2 was genetically engineered chimeric SARS-COV-1 that would be obvious. The closest known relative to SARS-COV-2 has actually recently been found in Laos [nature.com], and it even has SARS-COV-2's heretofore unique receptor binding proteins.
The problem all along with the "genetics experiment gone awry" conspiracy theory has been this: where did all the parts for this supposedly chimeric virus come from? You don't start with random viruses unknown to science; that leads your research to a universe of dead ends. At least some of the pieces you work with have to be known to science, otherwise you'd never get a result. PREEMPT may have been a terrible idea (or at least a now-controversial idea) that nobody wants to be associated with now, but it's not the origin of COVID-19.
People are attracted to conspiracy theories about COVID origins because CTs are simple to understand and actually comforting. How did this happen? Someone *bad* made this happen. But epidemiologists have been expecting some emergent respiratory virus to go pandemic for years now. If the answer is that humanity is simply vulnerable to emerging pathogens, that's not a comforting conclusion at all.
Re:Not if we don't try hard to port them to humans (Score:5, Informative)
All of which is highly improbable.
We can actualy rule out that it was "created in a lab". Gene splicing leaves large satelite repeat sequences as part of the process, and those dont exist on that genome.
Further, we have no capacity to design that spike (Which, by the way is wholy novel to SARS-COV-2). We can barely work out how to predict protein folds on simple molecules, let alone an absolutely monsterous molecule like the sars-cov-2 spike. In fact the folding problem is so intractible, there are mathematians that think its unsolveable.
So we can rule out the possibility that the spike was designed.
Its also *highly* unlikely that some sort of "gain of function" (that favorite term of the "i didnt finish highschool biology" set) was involved here because it still cant explain such a huge molecule as the spike. Its a theory that posits scientists engaging in some sort of miraculous creation-ex-nihilo.
Coupled with former western workers at the claimed lab saying that no, that is not what was being researched at the lab, and inspectors concluding that indeed the theory is highly unlikely, I think its safe to say that whole theory was a bust.
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It took just one virus to cripple the world's... (Score:2, Insightful)
FYI, viruses don't shut down economies. The world didn't shut down for spanish flu. The shut down part is optional. That doesn't make shut downs wrong, but the virus didn't do it.
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Correct. Hundreds of previous epidemics caused barely a ripple in economies.
Re:It took just one virus to cripple the world's.. (Score:5, Insightful)
I think it's the word "cripple" that you should be taking issue with there. If no shutdowns had been applied anywhere in the world then the economy would still have suffered to some extent due to workers taking sick leave, some percentage of them dying, and more risk-averse people changing their behaviour (and hence their spending). I'm not an economic or health modeller, so I won't speculate as to whether the net effect on the global economy would have been more or less, but the effect described here as "crippling" was a reduction in global GDP by a whopping 2.77% according to this data [statista.com]. Contrast with the bubonic plague (not viral, I know), which caused a reduction in the European workforce of tens of percent, and even then didn't really cripple the economy so much as empower the serfs and eventually cause cultural change.
Things to consider about RNA and DNA (Score:5, Interesting)
While it is true that many segments of the human genome contain what we think of as uncoded or not useful sequences, many of which are the result of prior viral attacks, it is also true that using mRNA, miRNA, siRNA, circRNA and other sequences generated by our DNA in response to certain conditions, that we theoretically have defenses against many of them.
They just haven't been expressed, because we don't need them.
Just because you haven't seen a virus before does not mean our DNA lacks defenses against it.
Re:Things to consider about RNA and DNA (Score:5, Informative)
The other thing is well, genetic transfers of information are a thing.
Bacteria have been well known to send little snippets of DNA to other bacteria, or even things like viruses - the bacteria would capture a virus, then inject its ring of DNA into the virus. The next thing the virus infects gets that little ring of DNA as well.
It works well for non-eukaryote cells (which lack a nucleus and basically have their genome in the cytoplasm), but the viral method is basically believed to be how we inherited a lot of our DNA. As we have eukaryote cells, random strands of DNA in the cell are basically destroyed because they shouldn't exist. Eukaryotes carry their DNA in the nucleus of the cell, and a copy to RNA is made in order to carry out cell processes. This is an excellent method of controlling infection.
Of course, nature evolves and viruses evolved to be able to carry their DNA into the nucleus and take over the cell machinery in order to operate. Or viruses evolved to use RNA instead - but then had to copy the mechanism to copy the RNA along with them, because eukaryotes cannot duplicate RNA.
The evolution of genetics at a high level is actually a fascinating subject to study
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While it is true that many segments of the human genome contain what we think of as uncoded or not useful sequences, many of which are the result of prior viral attacks, it is also true that using mRNA, miRNA, siRNA, circRNA and other sequences generated by our DNA in response to certain conditions, that we theoretically have defenses against many of them.
They just haven't been expressed, because we don't need them.
Just because you haven't seen a virus before does not mean our DNA lacks defenses against it.
Without active pressure from the viruses, though, mutations which inactivate those defenses will be evolutionarily neutral, meaning the defenses will degrade over time in the same way that the program to build working eyes degrades over time in cave fish. It'd be interesting to calculate how frequently a virus would have to show up in order to make deactivating mutations selectively negative enough to preserve the defenses in between attacks. (I guess the parallel would be calculating how often you'd have
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Without active pressure from the viruses, though, mutations which inactivate those defenses will be evolutionarily neutral, meaning the defenses will degrade over time in the same way that the program to build working eyes degrades over time in cave fish. It'd be interesting to calculate how frequently a virus would have to show up in order to make deactivating mutations selectively negative enough to preserve the defenses in between attacks. (I guess the parallel would be calculating how often you'd have to light up the cave in order for the fish to not lose their sight.)
True, but sometimes when we take medications which block the biochemical pathways, then we find some of the sequences from the secondary or tertiary pathways are activated, so they can, in fact, be expressed.
Of course, if that resistance is that far back, it might think you're a fish and do things in a way that isn't good for you, either.
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That would make an interesting paper for a journal
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Science has had a couple of papers last year addressing this. Antigen tests of the population of central China found that indeed, they appear to have been immunologically challenged by multiple unknown coronaviruses. And a study modeling the initial emergence of the pandemic, using the transmission characteristics of the initial virus, indicated that successfully establishing a pandemic was a somewhat unlikely event - multiple similar cross-overs will occur for every one that takes off. This is easily see
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There are zillions of viruses (Score:2)
Viruses are everywhere and pretty much every lifeform has parasitical viruses that target them but they are generally very specific to their hosts. And evolved in synchrony with them. There are way more than 100,000 viruses that we don't know anything about, but that doesn't mean they are a threat to us.
Yes it is entirely possible that some small fraction could mutate sufficiently to cross over to humans. Many of those we do know about. It would cost a few billion to develop vaccines against known zoonotic
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BTW, he was also the scientist who lead the WHO's meek attempt at identifying the virus' origin in China:
https://www.dailymail.co.uk/news/article-9129749/How-Peter-Daszak-WHOs-team-investigating-original-source-outbreak.html
You can't make this stuff up,
Re: Peter Dazak is probably co-responsible for Cov (Score:1)
He needs to be put against the nearest wall and shot.
Who is surprised? (Score:2)