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."
Starting this summer, the public buses in the Oberhaching suburb of Munich, Germany, won’t have to be plugged in to charge overnight anymore. Stefan Schelle, the mayor of Oberhaching, is taking advantage of the fact that an innovative startup has its offices in his community: Magment, short for “magnetizing cement,” will install its underground charging pad in the coming months. As soon as that happens, the buses will charge while they wait at the city’s main station or while stored at their overnight quarters.
In his light-filled office, Magment’s co-founder and CEO, Mauricio Esguerra, demonstrates how the new technology works: The lights on his black model car only flash when he puts the miniature Porsche directly atop the induction plate. “This works just like when you charge your iPhone on its charging pad or heat a pot on an induction range. People don’t have to be afraid of magnetic fields or anything like that,” says the 60-year-old Colombia-born entrepreneur. “The induction only gets activated when the storage battery is placed directly on top.
Patented by Esguerra, the “magnetizing concrete” is able to target the charge quite precisely. The batteries will be mounted in a box underneath the vehicles such as the retrofitted public buses. “Look, here’s one passing by,” says Esguerra, pointing out the window as a blue city bus rides past his office.
An invention finds its purpose
Esguerra grew up in Bogotá, studied physics at the Technical University Munich where he fell in love with a German woman, and started a family in her home country. For 15 years, he developed magnetic products, including the magnetizing cement, for Siemens, Europe’s largest industrial manufacturing company. The patent belonged to Siemens, of course. “But there were hardly any electric vehicles yet,” Esguerra says, “and Siemens didn’t quite know what to do with this invention.”
Esguerra changed companies a few times but, in 2015, he got an offer from Siemens. The patent for the magnetizing cement was expiring and Siemens wasn’t interested in keeping it. Would he, as the inventor, want it back? “I did not hesitate a second,” Esguerra remembers with a smile. “I’m a magnetician at heart.” That same year, he founded Magment to finally make use of the technology he created 20 years ago.
To demonstrate how his cement is made, he opens the lid of a plastic bucket filled with cement powder. Mixed in are fingernail-sized black pieces, so-called ferrites, mainly consisting of three ceramic oxides: iron, nickel and zinc. Conventionally, they are used in electronics such as cell phones, computers and cables. Molded in concrete, ferrites create a magnetic field that can transport charge to a vehicle, potentially eliminating range anxiety for EV drivers.
Molded in concrete, ferrites create a magnetic field that can transport charge to a vehicle, potentially eliminating range anxiety for EV drivers.
Magment
“Ferrites have extremely high rejection rates,” Esguerra adds. “It’s comparable to other ceramics: As soon as there is a small tear or crack, the material is rejected. We are talking about a rejection pile of 500,000 tons per year worldwide. There are mountains of unused materials.”
Exactly this fact was the starting point of his research at Siemens: “What can we do with this energy-intensive material? Back then, it was crushed up and mixed into the cement for building streets, without adding any function.” Today, too, the Magment material can simply be mixed with the conventional material and equipment of the cement industry. “We take advantage of the fact that we don’t have to build factories and don’t have high transportation costs."
In addition to saving resources, recycled ferrite also makes concrete more durable.
No plugs, no charging breaks
A young intern in the office next door winds cables around a new coil. These coils will later be lowered underground in a box, connected to the grid and encased in magnetizing concrete. The recipient box looks similar; it’s another coil but smaller, and it will be mounted underneath the carriage of the vehicle. For a car, the battery box would be 25 by 25 centimeters (about 10 inches), for a scooter five by five centimeters (about two inches).
Esguerra pushes an electric scooter into a cemented scooter rack next to his office. The charging pad is invisible. A faint beep is the only sign that it has started charging. “Childs play!” Esguerra says. “Even when someone puts in the scooter a little crooked, the charge still works. Our efficiency rate is up to 96 percent.” From this summer on, hotel chains in Munich will try out this system with their rental scooters, at a price of about 500 Euros per charging station.
Compared to plug-in charging, Magment’s benefits include smaller batteries that charge slower and, therefore, gentler, so they may last longer. Nobody needs to plug in the vehicles manually anymore. “Personally, I’ve had an EV for six years,” Esguerra says, “and how often does it happen that I forgot to plug it in overnight and then start out with a low charge in the morning? Once people get used to the invisible charging system, it will become the norm.“
There are also downsides: Most car companies aren’t ready for the new technology. Hyundai is the first carmaker that announced plans to equip some new models with inductive charging capability. “How many cars are electrified worldwide?” Esguerra asks and gives the answer himself: “One percent. And how many forklifts are electrified? More than 70 percent!” Therefore, Magment focuses on charging forklifts, e-scooters and buses.
Magment has focused most of its efforts on charging forklifts and other vehicle types that are entirely or predominantly electric, unlike cars.
Magment
On the morning of my visit to Esguerra’s office, a developer of the world’s third-biggest forklift manufacturer is there to inspect how the technology works on the ground. In the basement, a Magment engineer drives an electric forklift over a testbed with invisible charging coils, turning on the green charging light. Esguerra opens the interior of the forklift and points out the two batteries. “With our system, the forklift will only need one battery.” The savings, about 7,000 Euro per forklift, will pay for the installation of Magment’s charging system in warehouses, Esguerra calculates. “Less personnel and no unnecessary wait times for charging will lead to further savings,” he says.
To implement the new technology as efficiently as possible, Magment engineers began recording the transport routes of forklifts in warehouses. “It looks like spaghetti diagrams,” Esguerra explains. “Soon you get the areas where the forklifts pass or wait most frequently. This is where you install the chargers underground.” The forklifts will charge while in use, without having to pause for charging breaks. The method could also work for robots, for instance, in warehouses and distribution centers.
Roads of the future could be electric
Potential disadvantages might become apparent once the technology is more broadly in use. Therefore investors were initially reluctant, Esguerra admits. “Some are eager to be the first but most prefer to wait until the technology has been extensively used in real life.”
A clear hurdle today is that electrifying entire freeways with induction coils would cost at least 1 to 1.5 million Euros per kilometer. The German Department for Transportation even calculates overall costs of 14 to 47 million Euros per kilometer. So, the technology may only make sense for areas where vehicles pass or dwell the longest, like the Oberhaching train station or a busy interstate toll booth.
And yet, Magment is ramping up to compete with other companies that build larger inductive charging pads. The company just finished the first 20 meters of a testbed in Indiana, in partnership with the Purdue University and the Indiana Department of Transportation. Magment is poised to build “the world’s first contactless wireless-charging concrete pavement highway segment,” Purdue University announced.
The project, part of Purdue’s ASPIRE (Advancing Sustainability through Powered Infrastructure for Roadway Electrification) program, is financed by the National Science Foundation. “Indiana is known as the Crossroads of America, and we’re committed to fortifying our position as a transportation leader by innovating to support the emerging vehicle technology,” Governor Eric J. Holcomb said. If testing is successful, including the concrete’s capacity to charge heavy trucks operating at higher power (200 kilowatts and above), Indiana plans to identify a highway segment to install Magment’s charging pads. The earliest would be 2023 at best.
In the meantime, buses in the Californian Antelope Valley, trams at Hollywood's Universal Studios and transit buses in Tampa, Florida, are already charging with inductive technology developed by Wave, a company spun out of Utah State University. In Michigan, Governor Gretchen Whitmer announced plans to build a test route for vehicles to charge while driving, in collaboration with the Israel-based company Electreon, and this year contracted to build the first road-based charging system in the U.S. The state is providing support through an innovative grant program.
Costs remain one of the biggest obstacles, but Esguerra’s vision includes the potential that toll roads could charge a premium for inductive charging capabilities. “And in reverse, a driver who has too much energy could feed his surplus into the grid while driving,” Esguerra dreams.
Meanwhile, Wave’s upcoming big projects are moving trucks along a route in Southern California and running a UPS route between Seattle and Portland. Wave CTO Michael Masquelier describes the inductive power transfer his company champions as “similar to a tuning fork. By vibrating that fork, you sent energy through the air and it is received by another tuning fork across the room. So it’s similar to that, but it’s magnetic energy versus sound energy.”
He hopes to partner with Magment, saying that “the magnetizing cement makes installation easier and improves the energy efficiency.” More research is needed to evaluate which company’s technology will prove to be the most efficient, practical, and cost-effective.
Esguerra’s vision includes the potential that toll roads could charge a premium for inductive charging capabilities. “And in reverse, a driver who has too much energy could feed his surplus into the grid while driving,” Esguerra dreams.
The future will soon arrive in the idyllic town of Bad Staffelstein, a quaint tourist destination in the Upper Franconia region of Germany. Visitors will be taken to and from the main station and the popular thermal bath by driverless shuttles. Together with the University of Wuppertal, the regional government of Upper Franconia wants to turn its district into “the center of autonomous driving.” Magment is about to install inductive charging pads at the shuttle stations and the thermal bath, eliminating the need for the shuttles to stop for charging times. No more drivers, no cable, no range anxiety. Masquelier believes that “wireless and autonomous driving go hand in hand.” Science fiction? It will become science reality in spring 2023.
CORRECTION: An earlier version of the story erroneously mentioned that Electreon required overhead cables.
Smartwatches can track COVID-19 symptoms, study finds
If a COVID-19 infection develops, a wearable device may eventually be able to clue you in. A study at the University of Michigan found that a smartwatch can monitor how symptoms progress.
The study evaluated the effects of COVID-19 with various factors derived from heart-rate data. This method also could be employed to detect other diseases, such as influenza and the common cold, at home or when medical resources are limited, such as during a pandemic or in developing countries.
Tracking students and medical interns across the country, the University of Michigan researchers found that new signals embedded in heart rate indicated when individuals were infected with COVID-19 and how ill they became.
For instance, they discovered that individuals with COVID-19 experienced an increase in heart rate per step after the onset of their symptoms. Meanwhile, people who reported a cough as one of their COVID-19 symptoms had a much more elevated heart rate per step than those without a cough.
“We previously developed a variety of algorithms to analyze data from wearable devices. So, when the COVID-19 pandemic hit, it was only natural to apply some of these algorithms to see if we can get a better understanding of disease progression,” says Caleb Mayer, a doctoral student in mathematics at the University of Michigan and a co-first author of the study.
People may not internally sense COVID-19’s direct impact on the heart, but “heart rate is a vital sign that gives a picture of overall health," says Daniel Forger, a University of Michigan professor.
Millions of people are tracking their heart rate through wearable devices. This information is already generating a tremendous amount of data for researchers to analyze, says co-author Daniel Forger, professor of mathematics and research professor of computational medicine and bioinformatics at the University of Michigan.
“Heart rate is affected by many different physiological signals,” Forger explains. “For instance, if your lungs aren’t functioning properly, your heart may need to beat faster to meet metabolic demands. Your heart rate has a natural daily rhythm governed by internal biological clocks.” While people may not internally sense COVID-19’s direct impact on the heart, he adds that “heart rate is a vital sign that gives a picture of overall health.”
Among the total of 2,164 participants who enrolled in the student study, 72 undergraduate and graduate students contracted COVID-19, providing wearable data from 50 days before symptom onset to 14 days after. The researchers also analyzed this type of data for 43 medical interns from the Intern Health Study by the Michigan Neuroscience Institute and 29 individuals (who are not affiliated with the university) from the publicly available dataset.
Participants could wear the device on either wrist. They also documented their COVID-19 symptoms, such as fever, shortness of breath, cough, runny nose, vomiting, diarrhea, body aches, loss of taste, loss of smell, and sore throat.
Experts not involved in the study found the research to be productive. “This work is pioneering and reveals exciting new insights into the many important ways that we can derive clinically significant information about disease progression from consumer-grade wearable devices,” says Lisa A. Marsch, director of the Center for Technology and Behavioral Health and a professor in the Geisel School of Medicine at Dartmouth College. “Heart-rate data are among the highest-quality data that can be obtained via wearables.”
Beyond the heart, she adds, “Wearable devices are providing novel insights into individuals’ physiology and behavior in many health domains.” In particular, “this study beautifully illustrates how digital-health methodologies can markedly enhance our understanding of differences in individuals’ experience with disease and health.”
Previous studies had demonstrated that COVID-19 affects cardiovascular functions. Capitalizing on this knowledge, the University of Michigan endeavor took “a giant step forward,” says Gisele Oda, a researcher at the Institute of Biosciences at the University of Sao Paulo in Brazil and an expert in chronobiology—the science of biological rhythms. She commends the researchers for developing a complex algorithm that “could extract useful information beyond the established knowledge that heart rate increases and becomes more irregular in COVID patients.”
Wearable devices open the possibility of obtaining large-scale, long, continuous, and real-time heart-rate data on people performing everyday activities or while sleeping. “Importantly, the conceptual basis of this algorithm put circadian rhythms at the center stage,” Oda says, referring to the physical, mental, and behavioral changes that follow a 24-hour cycle. “What we knew before was often based on short-time heart rate measured at any time of day,” she adds, while noting that heart rate varies between day and night and also changes with activity.
However, without comparison to a control group of people having the common flu, it is difficult to determine if the heart-rate signals are unique to COVID-19 or also occur with other illnesses, says John Torous, an assistant professor of psychiatry at Harvard Medical School who has researched wearable devices. In addition, he points to recent data showing that many wearables, which work by beaming light through the skin, may be less accurate in people with darker skin due to variations in light absorption.
While the results sound interesting, they lack the level of conclusive evidence that would be needed to transform how physicians care for patients. “But it is a good step in learning more about what these wearables can tell us,” says Torous, who is also director of digital psychiatry at Beth Israel Deaconess Medical Center, a Harvard affiliate, in Boston. A follow-up step would entail replicating the results in a different pool of people to “help us realize the full value of this work.”
It is important to note that this research was conducted in university settings during the early phases of the pandemic, with remote learning in full swing amid strict isolation and quarantine mandates in effect. The findings demonstrate that physiological monitoring can be performed using consumer-grade wearable sensors, allowing research to continue without in-person contact, says Sung Won Choi, a professor of pediatrics at the University of Michigan who is principal investigator of the student study.
“The worldwide COVID-19 pandemic interrupted a lot of activities that relied on face-to-face interactions, including clinical research,” Choi says. “Mobile technology proved to be tremendously beneficial during that time, because it allowed us to collect detailed physiological data from research participants remotely over an entire semester.” In fact, the researchers did not have any in-person contact with the students involved in the study. “Everything was done virtually," Choi explains. "Importantly, their willingness to participate in research and share data during this historical time, combined with the capacity of secure cloud storage and novel mathematical analytics, enabled our research teams to identify unique patterns in heart-rate data associated with COVID-19.”