7 Things to Know about the U.S.’s Capability to Detect Omicron
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
If the new variant Omicron isn’t here already – which many experts suspect that it is – it will be soon. While we wait for scientists to conduct the necessary research to characterize its transmissibility, potential fitness at immune evasion, and disease severity, we wanted to give Leaps.org readers a window into how the U.S. is positioned to detect the variant. So we spoke to Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories, a membership organization that represents state and local government health labs in the United States. Here are seven insights she shared.
1) If you test positive for COVID-19 with a standard PCR test, the diagnostic report will not tell you which variant you have. There are no diagnostic tests available for your doctor to order to identify variants. To find out the variant, the specimen must be sent to a commercial, clinical, academic, or public health laboratory for genetic sequencing.
2) Today, the U.S. sequences about 5 to 10 percent of all diagnostic specimens that test positive for SARS-CoV-2 in order to determine which variants are circulating and where. Last week nationally, for example, labs sequenced about 80,000 samples. This represents a massive increase from last year at this time, when labs were only sequencing about 8,000 specimens per week. Currently, 99.5 percent of circulating SARS-CoV-2 virus in the U.S. is the Delta variant.
3) The U.S. is “very well prepared” to detect Omicron, Wroblewski says, “particularly compared to where we were when the Alpha variant, or B117 first emerged.” Of the hunt for Omicron, she adds, “it’s very reminiscent of that time, except we are doing so much more sequencing and we have so much better coverage with our sequencing geographically, and we're doing it in a much more timely way. We have the ability to find emerging variants that are circulating in 0.01 percent of the population.”
4) Deciding which specimens to sample is not totally random. Samples that have more virus are likely to lead to better sequencing results. Labs also look to have a diverse set of representative samples, meaning across geographic regions and across gender, race, ethnicity, and age groups. Clinical diversity is also important, such as including pregnant women, severe in-patient cases, mild cases, etc.
5) Sequencing more is not necessarily better to find Omicron faster. “We will increase the number of sequences to a certain extent,” Wroblewski says. “Where we exhibit some caution is doing that indiscriminately isn’t the most effective use of time and resources. The important thing is to try to find Omicron, and if you increase your testing capacity too much, right now, it's still predominantly Delta in the U.S. by a long shot. So you’re mostly going to sequence Delta and you run the risk of delaying your discovery of Omicron, if you focus solely on increasing sequencing.”
So besides just ramping up the sheer numbers of sequencing, diagnostic labs across the country are now advised to preferentially use a certain PCR test made by Thermo Fisher that can help hasten the detection of Omicron. It turns out that Omicron’s specific mutations in the Spike protein mean that the Spike is not picked up on this PCR test, which yields a type of result called an S-gene target failure. Yet the test will still accurately pick up a COVID-19 diagnosis, because it detects two other gene targets on Omicron that are not mutated. “That S-gene target failure gives you a good indication that you may have Omicron. It’s a good early screen.”
Labs will then still need to sequence the whole genome to confirm it matches the Omicron sequence. “So right now, the new recommendation is to use [the Thermo Fisher test] as much as possible to give us a better chance of detecting Omicron more quickly.”
6) This Thermo Fisher test is “fairly widely used” in the U.S. already, so many labs are already well positioned to make the shift. “In early to mid 2020,” Wroblewski explains, “when the supply chain issue for testing was acute, many public health labs implemented five, six, seven, eight different tests, just so they could get enough supplies to do all the testing. Now that we're in a much better place supply-chain wise, it's very difficult and time consuming and cumbersome to maintain all those different test methods all the time, and many, many labs scaled back to only one or two. And so this [new recommendation] would just be shifting to two for some labs that will be shifting to them.”
7) Once Omicron is found here, labs will be focused on finding as many cases as possible, and the CDC will be conducting a variety of studies to determine the impact of the variant on diagnostics, therapeutics, and vaccines. Epidemiologists at the local, state, and federal level will analyze which populations it is spreading in, as well as the severity of the disease it causes. They will work to sort out different impacts on vaccinated vs. unvaccinated populations. The ultimate goal, Wroblewski concludes, is to “use all of that information to make better public health decisions and inform the public about what’s going on.”
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
Fast for Longevity, with Less Hunger, with Dr. Valter Longo
You’ve probably heard about intermittent fasting, where you don’t eat for about 16 hours each day and limit the window where you’re taking in food to the remaining eight hours.
But there’s another type of fasting, called a fasting-mimicking diet, with studies pointing to important benefits. For today’s podcast episode, I chatted with Dr. Valter Longo, a biogerontologist at the University of Southern California, about all kinds of fasting, and particularly the fasting-mimicking diet, which minimizes hunger as much as possible. Going without food for a period of time is an example of good stress: challenges that work at the cellular level to boost health and longevity.
Listen on Apple | Listen on Spotify | Listen on Stitcher | Listen on Amazon | Listen on Google
If you’ve ever spent more than a few minutes looking into fasting, you’ve almost certainly come upon Dr. Longo's name. He is the author of the bestselling book, The Longevity Diet, and the best known researcher of fasting-mimicking diets.
With intermittent fasting, your body might begin to switch up its fuel type. It's usually running on carbs you get from food, which gets turned into glucose, but without food, your liver starts making something called ketones, which are molecules that may benefit the body in a number of ways.
With the fasting-mimicking diet, you go for several days eating only types of food that, in a way, keep themselves secret from your body. So at the level of your cells, the body still thinks that it’s fasting. This is the best of both worlds – you’re not completely starving because you do take in some food, and you’re getting the boosts to health that come with letting a fast run longer than intermittent fasting. In this episode, Dr. Longo talks about the growing number of studies showing why this could be very advantageous for health, as long as you undertake the diet no more than a few times per year.
Dr. Longo is the director of the Longevity Institute at USC’s Leonard Davis School of Gerontology, and the director of the Longevity and Cancer program at the IFOM Institute of Molecular Oncology in Milan. In addition, he's the founder and president of the Create Cures Foundation in L.A., which focuses on nutrition for the prevention and treatment of major chronic illnesses. In 2016, he received the Glenn Award for Research on Aging for the discovery of genes and dietary interventions that regulate aging and prevent diseases. Dr. Longo received his PhD in biochemistry from UCLA and completed his postdoc in the neurobiology of aging and Alzheimer’s at USC.
Show links:
Create Cures Foundation, founded by Dr. Longo: www.createcures.org
Dr. Longo's Facebook: https://www.facebook.com/profvalterlongo/
Dr. Longo's Instagram: https://www.instagram.com/prof_valterlongo/
Dr. Longo's book: The Longevity Diet
The USC Longevity Institute: https://gero.usc.edu/longevity-institute/
Dr. Longo's research on nutrition, longevity and disease: https://pubmed.ncbi.nlm.nih.gov/35487190/
Dr. Longo's research on fasting mimicking diet and cancer: https://pubmed.ncbi.nlm.nih.gov/34707136/
Full list of Dr. Longo's studies: https://pubmed.ncbi.nlm.nih.gov/?term=Longo%2C+Valter%5BAuthor%5D&sort=date
Research on MCT oil and Alzheimer's: https://alz-journals.onlinelibrary.wiley.com/doi/f...
Keto Mojo device for measuring ketones
Silkworms with spider DNA spin silk stronger than Kevlar
Story by Freethink
The study and copying of nature’s models, systems, or elements to address complex human challenges is known as “biomimetics.” Five hundred years ago, an elderly Italian polymath spent months looking at the soaring flight of birds. The result was Leonardo da Vinci’s biomimetic Codex on the Flight of Birds, one of the foundational texts in the science of aerodynamics. It’s the science that elevated the Wright Brothers and has yet to peak.
Today, biomimetics is everywhere. Shark-inspired swimming trunks, gecko-inspired adhesives, and lotus-inspired water-repellents are all taken from observing the natural world. After millions of years of evolution, nature has quite a few tricks up its sleeve. They are tricks we can learn from. And now, thanks to some spider DNA and clever genetic engineering, we have another one to add to the list.
The elusive spider silk
We’ve known for a long time that spider silk is remarkable, in ways that synthetic fibers can’t emulate. Nylon is incredibly strong (it can support a lot of force), and Kevlar is incredibly tough (it can absorb a lot of force). But neither is both strong and tough. In all artificial polymeric fibers, strength and toughness are mutually exclusive, and so we pick the material best for the job and make do.
Spider silk, a natural polymeric fiber, breaks this rule. It is somehow both strong and tough. No surprise, then, that spider silk is a source of much study.The problem, though, is that spiders are incredibly hard to cultivate — let alone farm. If you put them together, they will attack and kill each other until only one or a few survive. If you put 100 spiders in an enclosed space, they will go about an aggressive, arachnocidal Hunger Games. You need to give each its own space and boundaries, and a spider hotel is hard and costly. Silkworms, on the other hand, are peaceful and productive. They’ll hang around all day to make the silk that has been used in textiles for centuries. But silkworm silk is fragile. It has very limited use.
The elusive – and lucrative – trick, then, would be to genetically engineer a silkworm to produce spider-quality silk. So far, efforts have been fruitless. That is, until now.
We can have silkworms creating silk six times as tough as Kevlar and ten times as strong as nylon.
Spider-silkworms
Junpeng Mi and his colleagues working at Donghua University, China, used CRISPR gene-editing technology to recode the silk-creating properties of a silkworm. First, they took genes from Araneus ventricosus, an East Asian orb-weaving spider known for its strong silk. Then they placed these complex genes – genes that involve more than 100 amino acids – into silkworm egg cells. (This description fails to capture how time-consuming, technical, and laborious this was; it’s a procedure that requires hundreds of thousands of microinjections.)
This had all been done before, and this had failed before. Where Mi and his team succeeded was using a concept called “localization.” Localization involves narrowing in on a very specific location in a genome. For this experiment, the team from Donghua University developed a “minimal basic structure model” of silkworm silk, which guided the genetic modifications. They wanted to make sure they had the exactly right transgenic spider silk proteins. Mi said that combining localization with this basic structure model “represents a significant departure from previous research.” And, judging only from the results, he might be right. Their “fibers exhibited impressive tensile strength (1,299 MPa) and toughness (319 MJ/m3), surpassing Kevlar’s toughness 6-fold.”
A world of super-materials
Mi’s research represents the bursting of a barrier. It opens up hugely important avenues for future biomimetic materials. As Mi puts it, “This groundbreaking achievement effectively resolves the scientific, technical, and engineering challenges that have hindered the commercialization of spider silk, positioning it as a viable alternative to commercially synthesized fibers like nylon and contributing to the advancement of ecological civilization.”
Around 60 percent of our clothing is made from synthetic fibers like nylon, polyester, and acrylic. These plastics are useful, but often bad for the environment. They shed into our waterways and sometimes damage wildlife. The production of these fibers is a source of greenhouse gas emissions. Now, we have a “sustainable, eco-friendly high-strength and ultra-tough alternative.” We can have silkworms creating silk six times as tough as Kevlar and ten times as strong as nylon.
We shouldn’t get carried away. This isn’t going to transform the textiles industry overnight. Gene-edited silkworms are still only going to produce a comparatively small amount of silk – even if farmed in the millions. But, as Mi himself concedes, this is only the beginning. If Mi’s localization and structure-model techniques are as remarkable as they seem, then this opens up the door to a great many supermaterials.
Nature continues to inspire. We had the bird, the gecko, and the shark. Now we have the spider-silkworm. What new secrets will we unravel in the future? And in what exciting ways will it change the world?