COVID Variants Are Like “a Thief Changing Clothes” – and Our Camera System Barely Exists
Being able to track variants of concern in real time is crucial to our ability to stay ahead of the virus.
Whether it's "natural selection" as Darwin called it, or it's "mutating" as the X-Men called it, living organisms change over time, developing thumbs or more efficient protein spikes, depending on the organism and the demands of its environment. The coronavirus that causes COVID-19, SARS-CoV-2, is not an exception, and now, after the virus has infected millions of people around the globe for more than a year, scientists are beginning to see those changes.
The notorious variants that have popped up include B.1.1.7, sometimes called the UK variant, as well as P.1 and B.1.351, which seem to have emerged in Brazil and South Africa respectively. As vaccinations are picking up pace, officials are warning that now
is not the time to become complacent or relax restrictions because the variants aren't well understood.
Some appear to be more transmissible, and deadlier, while others can evade the immune system's defenses better than earlier versions of the virus, potentially undermining the effectiveness of vaccines to some degree. Genomic surveillance, the process of sequencing the genetic code of the virus widely to observe changes and patterns, is a critical way that scientists can keep track of its evolution and work to understand how the variants might affect humans.
"It's like a thief changing clothes"
It's important to note that viruses mutate all the time. If there were funding and personnel to sequence the genome of every sample of the virus, scientists would see thousands of mutations. Not every variant deserves our attention. The vast majority of mutations are not important at all, but recognizing those that are is a crucial tool in getting and staying ahead of the virus. The work of sequencing, analyzing, observing patterns, and using public health tools as necessary is complicated and confusing to those without years of specialized training.
Jeremy Kamil, associate professor of microbiology and immunology at LSU Health Shreveport, in Louisiana, says that the variants developing are like a thief changing clothes. The thief goes in your house, steals your stuff, then leaves and puts on a different shirt and a wig, in the hopes you won't recognize them. Genomic surveillance catches the "thief" even in those different clothes.
One of the tricky things about variants is recognizing the point at which they move from interesting, to concerning at a local level, to dangerous in a larger context.
Understanding variants, both the uninteresting ones and the potentially concerning ones, gives public health officials and researchers at different levels a useful set of tools. Locally, knowing which variants are circulating in the community helps leaders know whether mask mandates and similar measures should be implemented or discontinued, or whether businesses and schools can open relatively safely.
There's more to it than observing new variants
Analysis is complex, particularly when it comes to understanding which variants are of concern. "So the question is always if a mutation becomes common, is that a random occurrence?" says Phoebe Lostroh, associate professor of molecular biology at Colorado College. "Or is the variant the result of some kind of selection because the mutation changes some property about the virus that makes it reproduce more quickly than variants of the virus that don't have that mutation? For a virus, [mutations can affect outcomes like] how much it replicates inside a person's body, how much somebody breathes it out, whether the particles that somebody might breathe in get smaller and can lead to greater transmission."
Along with all of those factors, accurate and useful genomic surveillance requires an understanding of where variants are occurring, how they are related, and an examination of why they might be prevalent.
For example, if a potentially worrisome variant appears in a community and begins to spread very quickly, it's not time to raise a public health alarm until several important questions have been answered, such as whether the variant is spreading due to specific events, or if it's happening because the mutation has allowed the virus to infect people more efficiently. Kamil offered a hypothetical scenario to explain: Imagine that a member of a community became infected and the virus mutated. That person went to church and three more people were infected, but one of them went to a karaoke bar and while singing infected 100 other people. Examining the conditions under which the virus has spread is, therefore, an essential part of untangling whether a mutation itself made the virus more transmissible or if an infected person's behaviors contributed to a local outbreak.
One of the tricky things about variants is recognizing the point at which they move from interesting, to concerning at a local level, to dangerous in a larger context. Genomic sequencing can help with that, but only when it's coordinated. When the same mutation occurs frequently, but is localized to one region, it's a concern, but when the same mutation happens in different places at the same time, it's much more likely that the "virus is learning that's a good mutation," explains Kamil.
The process is called convergent evolution, and it was a fascinating topic long before COVID. Just as your heritage can be traced through DNA, so can that of viruses, and when separate lineages develop similar traits it's almost like scientists can see evolution happening in real time. A mutation to SARS-CoV-2 that happens in more than one place at once is a mutation that makes it easier in some way for the virus to survive and that is when it may become alarming. The widespread, documented variants P.1 and B.1.351 are examples of convergence because they share some of the same virulent mutations despite having developed thousands of miles apart.
However, even variants that are emerging in different places at the same time don't present the kind of threat SARS-CoV-2 did in 2019. "This is nature," says Kamil. "It just means that this virus will not easily be driven to extinction or complete elimination by vaccines." Although a person who has already had COVID-19 can be reinfected with a variant, "it is almost always much milder disease" than the original infection, Kamil adds. Rather than causing full-fledged disease, variants have the potiental to "penetrate herd immunity, spreading relatively quietly among people who have developed natural immunity or been vaccinated, until the virus finds someone who has no immunity yet, and that person would be at risk of hospitalization-grade severe disease or death."
Surveillance and predictions
According to Lostroh, genomic surveillance can help scientists predict what's going to happen. "With the British strain, for instance, that's more transmissible, you can measure how fast it's doubling in the population and you can sort of tell whether we should take more measures against this mutation. Should we shut things down a little longer because that mutation is present in the population? That could be really useful if you did enough sampling in the population that you knew where it was," says Lostroh. If, for example, the more transmissible strain was present in 50 percent of cases, but in another county or state it was barely present, it would allow for rolling lockdowns instead of sweeping measures.
Variants are also extremely important when it comes to the development, manufacture, and distribution of vaccines. "You're also looking at medical countermeasures, such as whether your vaccine is still effective, or if your antiviral needs to be updated," says Lane Warmbrod, a senior analyst and research associate at Johns Hopkins Center for Health Security.
Properly funded and extensive genomic surveillance could eventually help control endemic diseases, too, like the seasonal flu, or other common respiratory infections. Kamil says he envisions a future in which genomic surveillance allows for prediction of sickness just as the weather is predicted today. "It's a 51 for infection today at the San Francisco Airport. There's been detection of some respiratory viruses," he says, offering an example. He says that if you're a vulnerable person, if you're immune-suppressed for some reason, you may want to wear a mask based on the sickness report.
The U.S. has the ability, but lacks standards
The benefits of widespread genomic surveillance are clear, and the United States certainly has the necessary technology, equipment, and personnel to carry it out. But, it's not happening at the speed and extent it needs to for the country to gain the benefits.
"The numbers are improving," said Kamil. "We're probably still at less than half a percent of all the samples that have been taken have been sequenced since the beginning of the pandemic."
Although there's no consensus on how many sequences is ideal for a robust surveillance program, modeling performed by the company Illumina suggests about 5 percent of positive tests should be sequenced. The reasons the U.S. has lagged in implementing a sequencing program are complex and varied, but solvable.
Perhaps the most important element that is currently missing is leadership. In order to conduct an effective genomic surveillance program, there need to be standards. The Johns Hopkins Center for Health Security recently published a paper with recommendations as to what kinds of elements need to be standardized in order to make the best use of sequencing technology and analysis.
"Along with which bioinformatic pipelines you're going to use to do the analyses, which sequencing strategy protocol are you going to use, what's your sampling strategy going to be, how is the data is going to be reported, what data gets reported," says Warmbrod. Currently, there's no guidance from the CDC on any of those things. So, while scientists can collect and report information, they may be collecting and reporting different information that isn't comparable, making it less useful for public health measures and vaccine updates.
Globally, one of the most important tools in making the information from genomic surveillance useful is GISAID, a platform designed for scientists to share -- and, importantly, to be credited for -- their data regarding genetic sequences of influenza. Originally, it was launched as a database of bird flu sequences, but has evolved to become an essential tool used by the WHO to make flu vaccine virus recommendations each year. Scientists who share their credentials have free access to the database, and anyone who uses information from the database must credit the scientist who uploaded that information.
Safety, logistics, and funding matter
Scientists at university labs and other small organizations have been uploading sequences to GISAID almost from the beginning of the pandemic, but their funding is generally limited, and there are no standards regarding information collection or reporting. Private, for-profit labs haven't had motivation to set up sequencing programs, although many of them have the logistical capabilities and funding to do so. Public health departments are understaffed, underfunded, and overwhelmed.
University labs may also be limited by safety concerns. The SARS-CoV-2 virus is dangerous, and there's a question of how samples should be transported to labs for sequencing.
Larger, for-profit organizations often have the tools and distribution capabilities to safely collect and sequence samples, but there hasn't been a profit motive. Genomic sequencing is less expensive now than ever before, but even at $100 per sample, the cost adds up -- not to mention the cost of employing a scientist with the proper credentials to analyze the sequence.
The path forward
The recently passed COVID-19 relief bill does have some funding to address genomic sequencing. Specifically, the American Rescue Plan Act includes $1.75 billion in funding for the Centers for Disease Control and Prevention's Advanced Molecular Detection (AMD) program. In an interview last month, CDC Director Rochelle Walensky said that the additional funding will be "a dial. And we're going to need to dial it up." AMD has already announced a collaboration called the Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) Initiative that will bring together scientists from public health, academic, clinical, and non-profit laboratories across the country with the goal of accelerating sequencing.
Such a collaboration is a step toward following the recommendations in the paper Warmbrod coauthored. Building capacity now, creating a network of labs, and standardizing procedures will mean improved health in the future. "I want to be optimistic," she says. "The good news is there are a lot of passionate, smart, capable people who are continuing to work with government and work with different stakeholders." She cautions, however, that without a national strategy we won't succeed.
"If we maximize the potential and create that framework now, we can also use it for endemic diseases," she says. "It's a very helpful system for more than COVID if we're smart in how we plan it."
Chicken that is grown entirely in a laboratory, without harming a single bird, could be sold in supermarkets in the coming months. But critics say the doubts about lab-grown meat have not been appropriately explored.
Last November, when the U.S. Food and Drug Administration disclosed that chicken from a California firm called UPSIDE Foods did not raise safety concerns, it drily upended how humans have obtained animal protein for thousands of generations.
“The FDA is ready to work with additional firms developing cultured animal cell food and production processes to ensure their food is safe and lawful,” the agency said in a statement at the time.
Assuming UPSIDE obtains clearances from the U.S. Department of Agriculture, its chicken – grown entirely in a laboratory without harming a single bird – could be sold in supermarkets in the coming months.
“Ultimately, we want our products to be available everywhere meat is sold, including retail and food service channels,” a company spokesperson said. The upscale French restaurant Atelier Crenn in San Francisco will have UPSIDE chicken on its menu once it is approved, she added.
Known as lab-grown or cultured meat, a product such as UPSIDE’s is created using stem cells and other tissue obtained from a chicken, cow or other livestock. Those cells are then multiplied in a nutrient-dense environment, usually in conjunction with a “scaffold” of plant-based materials or gelatin to give them a familiar form, such as a chicken breast or a ribeye steak. A Dutch company called Mosa Meat claims it can produce 80,000 hamburgers derived from a cluster of tissue the size of a sesame seed.
Critics say the doubts about lab-grown meat and the possibility it could merge “Brave New World” with “The Jungle” and “Soylent Green” have not been appropriately explored.
That’s a far cry from when it took months of work to create the first lab-grown hamburger a decade ago. That minuscule patty – which did not contain any fat and was literally plucked from a Petri dish to go into a frying pan – cost about $325,000 to produce.
Just a decade later, an Israeli company called Future Meat said it can produce lab-grown meat for about $1.70 per pound. It plans to open a production facility in the U.S. sometime in 2023 and distribute its products under the brand name “Believer.”
Costs for production have sunk so low that researchers at Carnegie Mellon University in Pittsburgh expect sometime in early 2024 to produce lab-grown Wagyu steak to showcase the viability of growing high-end cuts of beef cheaply. The Carnegie Mellon team is producing its Wagyu using a consumer 3-D printer bought secondhand on eBay and modified to print the highly marbled flesh using a method developed by the university. The device costs $200 – about the same as a pound of Wagyu in the U.S. The initiative’s modest five-figure budget was successfully crowdfunded last year.
“The big cost is going to be the cells (which are being extracted by a cow somewhere in Pennsylvania), but otherwise printing doesn’t add much to the process,” said Rosalyn Abbott, a Carnegie Mellon assistant professor of bioengineering who is co-leader on the project. “But it adds value, unlike doing this with ground meat.”
Lab-Grown Meat’s Promise
Proponents of lab-grown meat say it will cut down on traditional agriculture, which has been a leading contributor to deforestation, water shortages and contaminated waterways from animal waste, as well as climate change.
An Oxford University study from 2011 concludes lab-grown meat could have greenhouse emissions 96 percent lower compared to traditionally raised livestock. Moreover, proponents of lab-grown meat claim that the suffering of animals would decline dramatically, as they would no longer need to be warehoused and slaughtered. A recently opened 26-story high-rise in China dedicated to the raising and slaughtering of pigs illustrates the current plight of livestock in stark terms.
Scientists may even learn how to tweak lab-grown meat to make it more nutritious. Natural red meat is high in saturated fat and, if it’s eaten too often, can lead to chronic diseases. In lab versions, the saturated fat could be swapped for healthier, omega-3 fatty acids.
But critics say the doubts about lab-grown meat and the possibility it could merge “Brave New World” with “The Jungle” and “Soylent Green” have not been appropriately explored.
A Slippery Slope?
Some academics who have studied the moral and ethical issues surrounding lab-grown meat believe it will have a tough path ahead gaining acceptance by consumers. Should it actually succeed in gaining acceptance, many ethical questions must be answered.
“People might be interested” in lab-grown meat, perhaps as a curiosity, said Carlos Alvaro, an associate professor of philosophy at the New York City College of Technology, part of the City University of New York. But the allure of traditionally sourced meat has been baked – or perhaps grilled – into people’s minds for so long that they may not want to make the switch. Plant-based meat provides a recent example of the uphill battle involved in changing old food habits, with Beyond Meat’s stock prices dipping nearly 80 percent in 2022.
"There are many studies showing that people don’t really care about the environment (to that extent)," Alvaro said. "So I don’t know how you would convince people to do this because of the environment.”
“From my research, I understand that the taste (of lab-grown meat) is not quite there,” Alvaro said, noting that the amino acids, sugars and other nutrients required to grow cultivated meat do not mimic what livestock are fed. He also observed that the multiplication of cells as part of the process “really mimic cancer cells” in the way they grow, another off-putting thought for would-be consumers of the product.
Alvaro is also convinced the public will not buy into any argument that lab-grown meat is more environmentally friendly.
“If people care about the environment, they either try and consume considerably less meat and other animal products, or they go vegan or vegetarian,” he said. “But there are many studies showing that people don’t really care about the environment (to that extent). So I don’t know how you would convince people to do this because of the environment.”
Ben Bramble, a professor at Australian National University who previously held posts at Princeton and Trinity College in Ireland, takes a slightly different tack. He noted that “if lab-grown meat becomes cheaper, healthier, or tastier than regular meat, there will be a large market for it. If it becomes all of these things, it will dominate the market.”
However, Bramble has misgivings about that occurring. He believes a smooth transition from traditionally sourced meat to a lab-grown version would allow humans to elide over the decades of animal cruelty perpetrated by large-scale agriculture, without fully reckoning with and learning from this injustice.
“My fear is that if we all switch over to lab-grown meat because it has become cheaper, healthier, or tastier than regular meat, we might never come to realize what we have done, and the terrible things we are capable of,” he said. “This would be a catastrophe.”
Bramble’s writings about cultured meat also raise some serious moral conundrums. If, for example, animal meat may be cultivated without killing animals, why not create products from human protein?
Actually, that’s already happened.
It occurred in 2019, when Orkan Telhan, a professor of fine arts at the University of Pennsylvania, collaborated with two scientists to create an art exhibit at the Philadelphia Museum of Art on the future of foodstuffs.
Although the exhibit included bioengineered bread and genetically modified salmon, it was an installation called “Ouroboros Steak” that drew the most attention. That was comprised of pieces of human flesh grown in a lab from cultivated cells and expired blood products obtained from online sources.
The exhibit was presented as four tiny morsels of red meat – shaped in patterns suggesting an ouroboros, a dragon eating its own tail. They were placed in tiny individual saucers atop a larger plate and placemat with a calico pattern, suggesting an item to order in a diner. The artwork drew international headlines – as well as condemnation for Telhan’s vision.
Telhan’s artwork is intended to critique the overarching assumption that lab-grown meat will eventually replace more traditional production methods, as well as the lack of transparency surrounding many processed foodstuffs. “They think that this problem (from industrial-scale agriculture) is going be solved by this new technology,” Telhan said. “I am critical (of) that perspective.”
Unlike Bramble, Telhan is not against lab-grown meat, so long as its producers are transparent about the sourcing of materials and its cultivation. But he believes that large-scale agricultural meat production – which dates back centuries – is not going to be replaced so quickly.
“We see this again and again with different industries, like algae-based fuels. A lot of companies were excited about this, and promoted it,” Telhan said. “And years later, we know these fuels work. But to be able to displace the oil industry means building the infrastructure to scale takes billions of dollars, and nobody has the patience or money to do it.”
Alvaro concurred on this point, which he believes is already weakened because a large swath of consumers aren’t concerned about environmental degradation.
“They’re going to have to sell this big, but in order to convince people to do so, they have to convince them to eat this product instead of regular meat,” Alvaro said.
Hidden Tweaks?
Moreover, if lab-based meat does obtain a significant market share, Telhan suggested companies may do things to the product – such as to genetically modify it to become more profitable – and never notify consumers. That is a particular concern in the U.S., where regulations regarding such modifications are vastly more relaxed than in the European Union.
“I think that they have really good objectives, and they aspire to good objectives,” Telhan said. “But the system itself doesn't really allow for that much transparency.”
No matter what the future holds, sometime next year Carnegie Mellon is expected to hold a press conference announcing it has produced a cut of the world’s most expensive beef with the help of a modified piece of consumer electronics. It will likely take place at around the same time UPSIDE chicken will be available for purchase in supermarkets and restaurants, pending the USDA’s approvals.
Abbott, the Carnegie Mellon professor, suggested the future event will be both informative and celebratory.
“I think Carnegie Mellon would have someone potentially cook it for us,” she said. “Like have a really good chef in New York City do it.”
In this week's Friday Five, breathing this way may cut down on anxiety, a fasting regimen that could make you sick, this type of job makes men more virile, 3D printed hearts could save your life, and the role of metformin in preventing dementia.
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Here are the promising studies covered in this week's Friday Five, featuring interviews with Dr. David Spiegel, associate chair of psychiatry and behavioral sciences at Stanford, and Dr. Filip Swirski, professor of medicine and cardiology at the Icahn School of Medicine at Mount Sinai.
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Here are the promising studies covered in this week's Friday Five, featuring interviews with Dr. David Spiegel, associate chair of psychiatry and behavioral sciences at Stanford, and Dr. Filip Swirski, professor of medicine and cardiology at the Icahn School of Medicine at Mount Sinai.
- Breathing this way cuts down on anxiety*
- Could your fasting regimen make you sick?
- This type of job makes men more virile
- 3D printed hearts could save your life
- Yet another potential benefit of metformin
* This video with Dr. Andrew Huberman of Stanford shows exactly how to do the breathing practice.