COVID Variants Are Like “a Thief Changing Clothes” – and Our Camera System Barely Exists
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."
Did researchers finally find a way to lick COVID?
Already vaccinated and want more protection from COVID-19? A protein found in ice cream could help, some research suggests, though there are a bunch of caveats.
The protein, called lactoferrin, is found in the milk of mammals and thus in dairy products, including ice cream. It has astounding antiviral properties that have been taken for granted and remain largely unexplored because it is a natural product, meaning that it cannot be patented and exploited by pharmaceutical companies.
Still, a few researchers in Europe and elsewhere have sought to better understand the compound.
Jonathan Sexton runs a drug screening program at the University of Michigan where cells are infected with a pathogen and then exposed to a library of the thousands of small molecule drug compounds – which can enter the body more easily than drugs with heavier molecules – approved by the FDA. In addition, the library includes compounds that passed phase 1 safety studies but later proved ineffective against the targeted disease. Each drug is dissolved in a solvent for exposure to the cells in the laborious testing process made feasible by robotic automation.
When COVID hit, researchers scrambled to identify any approved drug that might help fight the infection. Sexton decided to screen the drug library as well as some dietary supplements against SARS-CoV-2, the virus that causes the disease. Sexton says that the grunt work fell to Jesse Wotring, “a very talented PhD student,” who pulled lactoferrin off the shelf. But the regular solvent used in the testing process would destroy the protein, so he had to take another approach and do all the work by hand.
“We were agnostic,” says Sexton, who didn't have a strong interest in lactoferrin or any of the other compounds in the library, but the data was quite clear; lactoferrin “consistently produced the best efficacy...it was the absolute home run.” The findings were published in separate papers last year and in February.
It turns out that lactoferrin has several different mechanisms of action against SARS-CoV-2, inhibiting the virus from entering cells, moving around within them and replicating. Lactoferrin also modulates the overall immune response, which makes it difficult for the virus to simultaneously mutate resistance to the protein at every step of replication. “It has broad efficacy against every [SARS-CoV-2] variant that we've tested,” he says.
From bench to bedside
Sexton's initial interest was to develop a drug for the acute phase of COVID infection, to treat a hospitalized patient or prevent that hospitalization. But with the quick approval of vaccines and drugs to treat the disease, he increasingly focused on ways to better prevent infection and inhibit spread of the virus.
“If you can get lactoferrin to persist in your upper GI tract, then it may very well prevent the primary infection, and that's what we're really interested in.” He reasoned that a chewing gum formula might release enough lactoferrin into the mucosal tissue of the mouth and upper airways to inhibit replication and give the immune system a chance to knock out the virus before it can establish a foothold. It could also reduce the amount of virus spread through talking.
To get enough lactoferrin to have a possible beneficial effect, one would have to drink gallons of milk a day, “and that would have other undesirable consequences, like getting extremely obese,” says Sexton. Obesity is one of the leading risk factors for severe COVID disease.
Testing that theory has been difficult. The easiest way would be a “challenge trial,” where volunteers take the drug, or in this case gum, are exposed to the pathogen, and protection is measured. Some COVID challenge studies have been conducted in Europe but the FDA remains hesitant to allow such a study in the U.S. A traditional prevention study would be like a vaccine trial, involving thousands, perhaps tens of thousands of volunteers over a period of months or years, and it would be very expensive. No one has stepped forward to foot the bill.
So the next step for Sexton is a clinical trial of newly diagnosed COVID patients who will be given standard of care treatment, and layered on top of that they will receive either lactoferrin, probably in pill form, or a placebo. He has identified initial funding. “We would study their viral load over time as well as their symptoms.”
One issue the FDA is grappling with in considering the proposed trial is that it typically decides whether to approve drugs from a factory by applying a rigorous standard, called good manufacturing practices, while food products, which are the source of lactoferrin, are produced under somewhat different standards. The agency still has not finalized rules on how to deal with natural products used as drugs, such as fecal transplants, convalescent plasma, or medical marijuana.
Sexton is frustrated by the delay because lactoferrin derived from bovine milk whey has been used for many decades as a protein supplement by athletes, it is a large component of most infant formula, and the largest number of clinical studies of lactoferrin involve premature infants. There is no question of its safety, he says.
Do it yourself
So what can you do while waiting for regulatory wheels to spin and clinical trial data to be generated?
Could a dose of Ben & Jerry's provide some protection against SARS-CoV-2?
Sexton chuckles at the suggestion. He supposes it couldn't hurt. But to get enough lactoferrin to have a possible beneficial effect, one would have to drink gallons of milk a day, “and that would have other undesirable consequences, like getting extremely obese.” Obesity is one of the leading risk factors for severe COVID disease.
Pseudo-milk products made from soy, almonds, oats, or other plant products do not contain lactoferrin; it has to come from a teat. So that rules them out.
Whey-based protein shakes might be a useful way to add lactoferrin to the diet.
Probably the best option is to take conventional gelatin capsules of lactoferrin that are widely available wherever supplements are sold. Sexton calculates that about a gram a day, four 250 milligram capsules, should do it. He advises two in the morning and two a night. “You really want to take them on an empty stomach...your stomach treats [the lactoferrin protein] like it would a steak” and chops it for absorption in the intestine, which you do not want. About 70 percent of lactoferrin can get through an empty stomach, but eating food cranks up digestive gastric acids and the amount of intact lactoferrin that gets through to the gut plummets.
Sexton cautions, “We have not determined clinical efficacy yet,” and he is not offering advice as a physician, but in the spirit of harm reduction, he realizes that some people are going to try things that might help them. Lactoferrin “is remarkably safe. And so people have to make their own decisions about what they are willing to take and what they are not,” he says.
My guest today for the Making Sense of Science podcast is Camila dos Santos, associate professor at Cold Spring Harbor Lab, who is a leading researcher of the inner lives of human mammary glands, more commonly known as breasts. These organs are unlike any other because throughout life they undergo numerous changes, first in puberty, then during pregnancies and lactation periods, and finally at the end of the cycle, when babies are weaned. A complex interplay of hormones governs these processes, in some cases increasing the risk of breast cancer and sometimes lowering it. Witnessing the molecular mechanics behind these processes in humans is not possible, so instead Dos Santos studies organoids—the clumps of breast cells donated by patients who undergo breast reduction surgeries or biopsies.
Show notes:
2:52 In response to hormones that arise during puberty, the breast cells grow and become more specialized, preparing the tissue for making milk.
7:53 How do breast cells know when to produce milk? It’s all governed by chemical messaging in the body. When the baby is born, the brain will release the hormone called oxytocin, which will make the breast cells contract and release the milk.
12:40 Breast resident immune cells are including T-cells and B-cells, but because they live inside the breast tissue their functions differ from the immune cells in other parts of the body,
17:00 With organoids—dimensional clumps of cells that are cultured in a dish—it is possible to visualize and study how these cells produce milk.
21:50 Women who are pregnant later in life are more likely to require medical intervention to breastfeed. Scientists are trying to understand the fundamental reasons why it happens.
26:10 Breast cancer has many risks factors. Generic mutations play a big role. All of us have the BRCA genes, but it is the alternation in the DNA sequence of the BRCA gene that can increase the predisposition to breast cancer. Aging and menopause are the risk factors for breast cancer, and so are pregnancies.
29:22 Women that are pregnant before the age of 20 to 25, have a decreased risk of breast cancer. And the hypothesis here is that during pregnancy breast cells more specialized, as specialized cells, they have a limited lifespan. It's more likely that they die before they turn into cancer.
33:08 Organoids are giving scientists an opportunity to practice personalized medicine. Scientists can test drugs on organoids taken from a patient to identify the most efficient treatment protocol.
Links:
Camila dos Santos’s Lab Page.
Editor's note: In addition to being a regular writer for Leaps.org, Lina Zeldovich is the guest host for today's episode of the Making Sense of Science podcast.
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.