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Tag: virus
Free-electron lasers provide femtosecond X-ray pulses with a peak brilliance 10 billion times higher than any previously available X-ray source. such pulses could outrun key damage processes and allow structure determination without the need for crystallization and would be sufficient to image HIV, influenza and herpes, and further improvements may soon allow researchers to tackle the study of single proteins
it would be a huge improvement if you don’t need to grow crystals.
A code hidden in single-stranded RNA viruses tells the virus how to pack itself within its outer shell of proteins. the code causes >1B infections every year and there’s a chance to disrupt it.
The scientists decided to return to the human genome and search for K111. They isolated DNA from their HIV patients, as well as from healthy people. Remarkably, the scientists didn’t find just 1 copy of K111 in each of their subject’s genomes, as is the case in chimps. The more the scientists looked, the more variants they found. Some K111 viruses were fairly intact, while others were vestiges. The scientists found over 100 copies of the virus in the human genome, scattered across 15 chromosomes.
This finding suggests that between 6 ma and 800 ka ago, K111 was duplicated a few times at a fairly slow pace. It’s possible that Markowitz and his colleagues missed some other copies because the reconstruction of those ancient genomes wasn’t quite accurate enough for their search. But even if we generously assumed that Neanderthals and Denisovans had 20 K111 viruses apiece, that’s still a small fraction of the 100 or more copies of K111 the scientists found in the human genome. It was only later, in the past 800 ka, that K111 started proliferating at a faster pace.1 reason that K111 has gone overlooked till now is that it found a good place to hide–the center of chromosomes. This region, called the centromere, is a genomic Bermuda Triangle. It’s loaded with lots of short, repetitive stretches of DNA. When scientists reconstruct the sequence of a genome, they break DNA down into many overlapping segments, which they then try to rebuild based on overlapping similarities. Centromere DNA is so similar to itself that it’s easy to line up fragments in many different arrangements. As a result, centromeres make up much of the last 5% of the human genome that has yet to be mapped.
The Centers for Disease Control and Prevention rushed to complete a computer program it had been developing to track outbreaks; the program needed to be translated into French so it could be used in Guinea. The C.D.C. also dispatched a team, which grew to more than 12 and was led by Rollin, who arrived in Guinea on March 30. Some 3000 biohazard suits were flown in. Experts and volunteers poured in from the World Health Organization and the Red Cross.
The international health community doesn’t seem to have strong internet technologies, and wastes too much time forwarding shit to each other. In the US, there are too many dumb laws like HIPPA to make rational systems possible, but surely that’s not the case around the world?
Without additional interventions or changes in community behavior, CDC estimates that by January 20, 2015, there will be a total of ~1.4M Ebola cases in Liberia and Sierra Leone
It’s not looking good, between the rock (hard to get around, poor communications, not enough trained workers) and the hard place (religious practices that require touching the dead).
2015-05-11: That sounds like movie-plot science but is apparently real.
When he was released from Emory University Hospital in October after a long, brutal fight with Ebola that nearly ended his life, Dr. Ian Crozier’s medical team thought he was cured. But less than 2 months later, he was back at the hospital with fading sight, intense pain and soaring pressure in his left eye. Test results were chilling: The inside of Dr. Crozier’s eye was teeming with Ebola.
2015-08-13: There’s now a Ebola vaccine, which is great news. Let’s hope there’s never an outbreak in southern California with all the anti vaxxers there.
The outbreak of Ebola fever in Guinea, Liberia and Sierra Leone, which has killed more than 11K people, has dropped out of the news as it has been brought under control. Although new cases are now measured in 10s, rather than 100s, a week, the disease has not been stamped out—and a new epidemic could flare up somewhere else at any time. A vaccine against the virus responsible would be of enormous value. And a paper in the Lancet suggests one is now available.
See also
Ebola is no longer an incurable horror disease. The new vaccine, rVSV-ZEBOV, was used in the last outbreak in the Republic of Congo. It protected over 90K. Health responders deployed it in social rings: firstly those in contact with known cases, then their contacts. It’s the same strategy used against smallpox 40 years ago. And that was wiped out.
Amid unrelenting chaos and violence, scientists and doctors in the Democratic Republic of Congo have been running a clinical trial of new drugs to try to combat a year-long Ebola outbreak. On Monday, the trial’s cosponsors at the World Health Organization and the National Institutes of Health announced that 2 of the experimental treatments appear to dramatically boost survival rates.
these viruses “represent a form of life that either predated or coexisted with the most recent organism from which all other organisms on Earth are descended. If giant viruses are as old as Caetano-Anolles’ calculated, the implications are staggering. It means that a giant virus or one of its ancestors existed before other types of life and may have played a major role in shaping life as we know it. This could mean that viruses are one of the dominant evolutionary forces on this planet and that each organism has a deep, viral past.
2021-09-01: See also Giruses, giant viruses, which may have been there since the beginning.
soon it may even be possible to make evolutionary forecasts. Scientists may not be able to predict what life will be like 100 million years from now, but they may be able to make short-term forecasts for the next few months or years. And if they’re making predictions about viruses or other health threats, they might be able to save some lives in the process.
a procedure to predict influenza mutations every year with 90% precision, helping to produce the right vaccines for that season.
We can analyze any mutation, even those that haven’t been identified yet. This allows researchers to predict whether a novel mutation is likely to be dangerous or harmless — in essence, performing a screening test
and another one
10 years of work at Johns Hopkins has yielded a computer program that predicts, with far more accuracy than current methods, which mutations are likely to have the largest effect on the activity of the “dimmer switches” (which alter the cell’s gene activity) in DNA — suggesting new targets for diagnosis and treatment of many diseases.
i’m not one for moral panics, but this pathogen research is troubling:
The scientific benefit of making viruses more pathogenic is debatable: research tends to use old strains (may not be applicable to our current situation), there is a bias towards more spectacular and lethal virulence because it gets published and funded, there is no reason to think evolution will move in the same way (it is highly contingent, and hence what is learned may not help make vaccines or drugs), and the key experiment (doing it with humans) is unethical, and hence unfalsifiable. The ethics is also really problematic, since the rate of lab releases is not negligible and a flu outbreak can easily kill people – it has a skew distribution with a heavy tail.
Vecoy’s virus traps could be tailored to address emerging new viral outbreaks quickly and efficiently
If this works, it could have an impact on the scale of Louis Pasteur.
Scientists estimate that among all the viruses that infect all the animals of the world there may be around 800K which could, in the right circumstances, jump from their habitual hosts into humans and start spreading. Could all of them be identified, too, and sentry posts set up that would provide news of their incursions? The Global Immunological Observatory would ideally test every tiny sample of blood for 100Ks of distinct antibodies. Considering how hard large-scale testing for just sars-cov-2 has proved, this might seem impossibly ambitious.
After the pandemic, there will still be new strains of flu and other viruses to code. There will be a backlog of sequencing work for cancer and prenatal health and rare genetic diseases. There will be an ongoing surveillance effort for SARS-CoV-2 variants. An even bigger job, moreover, involves a continuing project to sequence untold strains of microbes, a project that Ginkgo has been involved with in search of new pharmaceuticals.
now that sequencing is cheap, it will move out of the lab and in situ:
Multiple appliances could benefit from integration with sequencing
sensors, including air conditioning or the main water supply to monitor harmful pathogens
2022-05-04: Bill Gates on how to prevent the next pandemic. He also wrote a book about it. Strangely, he has a misplaced belief in the WHO, which completely failed us.
If we’re going to make COVID-19 the last pandemic, the world needs to get to work right away on 3 key areas:
1. Make and deliver better tools.
1 key step is to create a library of antiviral compounds that are designed to attack common respiratory viruses, so that we can more easily find out if an existing drug will work in the event of an outbreak. We should also expand incentives for generics manufacturers to create low-cost versions of new drugs. We also need to support work on new types of tests that make it easier to collect samples and turn around results quickly, like better versions of the rapid antigen tests that many of us now take at home for COVID or even handheld devices that health workers can use to easily test people in their community.2. Improve disease monitoring.
Creating the GERM—Global Epidemic Response and Mobilization—team is one of the most important steps we can take to stop the next pandemic. GERM will play a crucial role in virtually every aspect of pandemic prevention, but improving monitoring will be the most significant part of their mandate.3. Strengthen health systems.
There are steps that countries at every income level should consider, like improving primary health care and deciding in advance of a crisis who will oversee what. Governments and donors also need a global forum where they can coordinate action with poor countries.
By feeding biological data about the various types of bats — their diet, the length of their wings, and so on — into their computer, they created a model that could offer predictions about the bats most likely to harbor betacoronaviruses. They found over 300 species that fit the bill.
Since that prediction in 2020, researchers have indeed found betacoronaviruses in 47 species of bats — all of which were on the prediction lists produced by some of the computer models they had created for their study. It was striking the way simple features such as body size could lead to powerful predictions about viruses. “A lot of it is the low-hanging fruit of comparative biology”.
the famous WI-38 stem cell line was started from an aborted fetus in 1962.
Vaccines made using WI-38 cells have immunized 100Ms of people against rubella, rabies, adenovirus, polio, measles, chickenpox and shingles.
I hope this pans out. That would be extra amazing.
Current flu vaccines use inactivated whole viruses and must be regularly remade to target the strains most likely to cause illness in the coming year. But the new nanoparticles would require fewer updates because they induce the production of antibodies that neutralize a wider range of flu strains. They could even protect against varieties of flu that have not yet emerged.
2020-12-08: Targeting the stalk
The beauty part of this vaccine is that it’s not only broad, but multifunctional with stalk-specific antibodies that can neutralize many kinds of influenza viruses. This universal vaccine could be particularly beneficial to low and middle income countries that don’t have the resources or the logistics to vaccinate their populations each year against influenza.
Gregor J. Rothfuss 