Scientists Are Growing an Edible Cholera Vaccine in Rice
The world's attention has been focused on the coronavirus crisis but Yemen, Bangladesh and many others countries in Asia and Africa are also in the grips of another pandemic: cholera. The current cholera pandemic first emerged in the 1970s and has devastated many communities in low-income countries. Each year, cholera is responsible for an estimated 1.3 million to 4 million cases and 21,000 to 143,000 deaths worldwide.
Immunologist Hiroshi Kiyono and his team at the University of Tokyo hope they can be part of the solution: They're making a cholera vaccine out of rice.
"It is much less expensive than a traditional vaccine, by a long shot."
Cholera is caused by eating food or drinking water that's contaminated by the feces of a person infected with the cholera bacteria, Vibrio cholerae. The bacteria produces the cholera toxin in the intestines, leading to vomiting, diarrhea and severe dehydration. Cholera can kill within hours of infection if it if's not treated quickly.
Current cholera vaccines are mainly oral. The most common oral are given in two doses and are made out of animal or insect cells that are infected with killed or weakened cholera bacteria. Dukoral also includes cells infected with CTB, a non-harmful part of the cholera toxin. Scientists grow cells containing the cholera bacteria and the CTB in bioreactors, large tanks in which conditions can be carefully controlled.
These cholera vaccines offer moderate protection but it wears off relatively quickly. Cold storage can also be an issue. The most common oral vaccines can be stored at room temperature but only for 14 days.
"Current vaccines confer around 60% efficacy over five years post-vaccination," says Lucy Breakwell, who leads the U.S. Centers for Disease Control and Prevention's cholera work within Global Immunization Division. Given the limited protection, refrigeration issue, and the fact that current oral vaccines require two disease, delivery of cholera vaccines in a campaign or emergency setting can be challenging. "There is a need to develop and test new vaccines to improve public health response to cholera outbreaks."
A New Kind of Vaccine
Kiyono and scientists at Tokyo University are creating a new, plant-based cholera vaccine dubbed MucoRice-CTB. The researchers genetically modify rice so that it contains CTB, a non-harmful part of the cholera toxin. The rice is crushed into a powder, mixed with saline solution and then drunk. The digestive tract is lined with mucosal membranes which contain the mucosal immune system. The mucosal immune system gets trained to recognize the cholera toxin as the rice passes through the intestines.
The cholera toxin has two main parts: the A subunit, which is harmful, and the B subunit, also known as CTB, which is nontoxic but allows the cholera bacteria to attach to gut cells. By inducing CTB-specific antibodies, "we might be able to block the binding of the vaccine toxin to gut cells, leading to the prevention of the toxin causing diarrhea," Kiyono says.
Kiyono studies the immune responses that occur at mucosal membranes across the body. He chose to focus on cholera because he wanted to replicate the way traditional vaccines work to get mucosal membranes in the digestive tract to produce an immune response. The difference is that his team is creating a food-based vaccine to induce this immune response. They are also solely focusing on getting the vaccine to induce antibodies for the cholera toxin. Since the cholera toxin is responsible for bacteria sticking to gut cells, the hope is that they can stop this process by producing antibodies for the cholera toxin. Current cholera vaccines target the cholera bacteria or both the bacteria and the toxin.
David Pascual, an expert in infectious diseases and immunology at the University of Florida, thinks that the MucoRice vaccine has huge promise. "I truly believe that the development of a food-based vaccine can be effective. CTB has a natural affinity for sampling cells in the gut to adhere, be processed, and then stimulate our immune system, he says. "In addition to vaccinating the gut, MucoRice has the potential to touch other mucosal surfaces in the mouth, which can help generate an immune response locally in the mouth and distally in the gut."
Cost Effectiveness
Kiyono says the MucoRice vaccine is much cheaper to produce than a traditional vaccine. Current vaccines need expensive bioreactors to grow cell cultures under very controlled, sterile conditions. This makes them expensive to manufacture, as different types of cell cultures need to be grown in separate buildings to avoid any chance of contamination. MucoRice doesn't require such an expensive manufacturing process because the rice plants themselves act as bioreactors.
The MucoRice vaccine also doesn't require the high cost of cold storage. It can be stored at room temperature for up to three years unlike traditional vaccines. "Plant-based vaccine development platforms present an exciting tool to reduce vaccine manufacturing costs, expand vaccine shelf life, and remove refrigeration requirements, all of which are factors that can limit vaccine supply and accessibility," Breakwell says.
Kathleen Hefferon, a microbiologist at Cornell University agrees. "It is much less expensive than a traditional vaccine, by a long shot," she says. "The fact that it is made in rice means the vaccine can be stored for long periods on the shelf, without losing its activity."
A plant-based vaccine may even be able to address vaccine hesitancy, which has become a growing problem in recent years. Hefferon suggests that "using well-known food plants may serve to reduce the anxiety of some vaccine hesitant people."
Challenges of Plant Vaccines
Despite their advantages, no plant-based vaccines have been commercialized for human use. There are a number of reasons for this, ranging from the potential for too much variation in plants to the lack of facilities large enough to grow crops that comply with good manufacturing practices. Several plant vaccines for diseases like HIV and COVID-19 are in development, but they're still in early stages.
In developing the MucoRice vaccine, scientists at the University of Tokyo have tried to overcome some of the problems with plant vaccines. They've created a closed facility where they can grow rice plants directly in nutrient-rich water rather than soil. This ensures they can grow crops all year round in a space that satisfies regulations. There's also less chance for variation since the environment is tightly controlled.
Clinical Trials and Beyond
After successfully growing rice plants containing the vaccine, the team carried out their first clinical trial. It was completed early this year. Thirty participants received a placebo and 30 received the vaccine. They were all Japanese men between the ages of 20 and 40 years old. 60 percent produced antibodies against the cholera toxin with no side effects. It was a promising result. However, there are still some issues Kiyono's team need to address.
The vaccine may not provide enough protection on its own. The antigen in any vaccine is the substance it contains to induce an immune response. For the MucoRice vaccine, the antigen is not the cholera bacteria itself but the cholera toxin the bacteria produces.
"The development of the antigen in rice is innovative," says David Sack, a professor at John Hopkins University and expert in cholera vaccine development. "But antibodies against only the toxin have not been very protective. The major protective antigen is thought to be the LPS." LPS, or lipopolysaccharide, is a component of the outer wall of the cholera bacteria that plays an important role in eliciting an immune response.
The Japanese team is considering getting the rice to also express the O antigen, a core part of the LPS. Further investigation and clinical trials will look into improving the vaccine's efficacy.
Beyond cholera, Kiyono hopes that the vaccine platform could one day be used to make cost-effective vaccines for other pathogens, such as norovirus or coronavirus.
"We believe the MucoRice system may become a new generation of vaccine production, storage, and delivery system."
You're lying in bed late at night, the foggy swirl of the pandemic's 8th month just beginning to fall behind you, when you detect a slight tickle at the back of your throat.
"If half of people choose to use these tests every other day, then we can stop transmission faster than a vaccine can."
Suddenly fully awake, a jolt of panicked electricity races through your body. Has COVID-19 come for you? In the U.S., answering this simple question is incredibly difficult.
Now, you might have to wait for hours in line in your car to get a test for $100, only to find out your result 10-14 days later -- much too late to matter in stopping an outbreak. Due to such obstacles, a recent report in JAMA Internal Medicine estimated that 9 out of 10 infections in the U.S. are being missed.
But what if you could use a paper strip in the privacy of your own home, like a pregnancy test, and find out if you are contagious in real time?
e25 Bio, a small company in Cambridge, Mass., has already created such a test and it has been sitting on a lab bench, inaccessible, since April. It is an antigen test, which looks for proteins on the outside of a virus, and can deliver results in about 15 minutes. Also like an over-the-counter pregnancy test, e25 envisions its paper strips as a public health screening tool, rather than a definitive diagnostic test. People who see a positive result would be encouraged to then seek out a physician-administered, gold-standard diagnostic test: the more sensitive PCR.
Typically, hospitals and other health facilities rely on PCR tests to diagnose viruses. This test can detect small traces of genetic material that a virus leaves behind in the human body, which tells a clinician that the patient is either actively infected with or recently cleared that virus. PCR is quite sensitive, meaning that it is able to detect the presence of a virus' genetic material very accurately.
But although PCR is the gold-standard for diagnostics, it's also the most labor-intensive way to test for a virus and takes a relatively long time to produce results. That's not a good match for stopping super-spreader events during an unchecked pandemic. PCR is also not great at identifying the infected people when they are most at risk of potentially transmitting the virus to others.
That's because the viral threshold at which PCR can detect a positive result is so low, that it's actually too sensitive for the purposes of telling whether someone is contagious.
"The majority of time someone is PCR positive, those [genetic] remnants do not indicate transmissible virus," epidemiologist Michael Mina recently Tweeted. "They indicate remnants of a recently cleared infection."
To stop the chain of transmission for COVID-19, he says, "We need a more accurate test than PCR, that turns positive when someone is able to transmit."
In other words, we need a test that is better at detecting whether a person is contagious, as opposed to whether a small amount of virus can be detected in their nose or saliva. This kind of test is especially critical given the research showing that asymptomatic and pre-symptomatic people have high viral loads and are spreading the virus undetected.
The critical question for contagiousness testing, then, is how big a dose of SARS-CoV-2, the virus that causes COVID, does it take to infect most people? Researchers are still actively trying to answer this. As Angela Rasmussen, a coronavirus expert at Columbia University, told STAT: "We don't know the amount that is required to cause an infection, but it seems that it's probably not a really, really small amount, like measles."
Amesh Adalja, an infectious disease physician and a senior scholar at the Johns Hopkins University Center for Health Security, told LeapsMag: "It's still unclear what viral load is associated with contagiousness but it is biologically plausible that higher viral loads, in general, are associated with more efficient transmission especially in symptomatic individuals. In those without symptoms, however, the same relationship may not hold and this may be one of the reasons young children, despite their high viral loads, are not driving outbreaks."
"Antigen tests work best when there's high viral loads. They're catching people who are super spreaders."
Mina and colleagues estimate that widespread use of weekly cheap, rapid tests that are 100 times less sensitive than PCR tests would prevent outbreaks -- as long as the people who are positive self-isolate.
So why can't we buy e25Bio's test at a drugstore right now? Ironically, it's barred for the very reason that it's useful in the first place: Because it is not sensitive enough to satisfy the U.S. Food and Drug Administration, according to the company.
"We're ready to go," says Carlos-Henri Ferré, senior associate of operations and communications at e25. "We've applied to FDA, and now it's in their hands."
The problem, he said, is that the FDA is evaluating applications for antigen tests based on criteria for assessing diagnostics, like PCR, even when the tests serve a different purpose -- as a screening tool.
"Antigen tests work best when there's high viral loads," Ferré says. "They're catching people who are super spreaders, that are capable of continuing the spread of disease … FDA criteria is for diagnostics and not this."
FDA released guidance on July 29th -- 140 days into the pandemic -- recommending that at-home tests should perform with at least 80 percent sensitivity if ordered by prescription, and at least 90 percent sensitivity if purchased over the counter. "The danger of a false negative result is that it can contribute to the spread of COVID-19," according to an FDA spokesperson. "However, oversight of a health care professional who reviews the results, in combination with the patient's symptoms and uses their clinical judgment to recommend additional testing, if needed, among other things, can help mitigate some risks."
Crucially, the 90 percent sensitivity recommendation is judged upon comparison to PCR tests, meaning that if a PCR test is able to detect virus in 100 samples, the at-home antigen test would need to detect virus in at least 90 of those samples. Since antigen tests only detect high viral loads, frustrated critics like Mina say that such guidance is "unreasonable."
"The FDA at this moment is not understanding the true potential for wide-scale frequent testing. In some ways this is not their fault," Mina told LeapsMag. "The FDA does not have any remit to evaluate tests that fall outside of medical diagnostic testing. The proposal I have put forth is not about diagnostic testing (leave that for symptomatic cases reporting to their physician and getting PCR tests)....Daily rapid tests are not about diagnosing people and they are not about public health surveillance and they are not about passports to go to school, out to dinner or into the office. They are about reducing population-level transmission given a similar approach as vaccines."
A reasonable standard, he added, would be to follow the World Health Organization's Target Product Profiles, which are documents to help developers build desirable and minimally acceptable testing products. "A decent limit," Mina says, "is a 70% or 80% sensitivity (if they truly require sensitivity as a metric) to detect virus at Ct values less than 25. This coincides with detection of the most transmissible people, which is important."
(A Ct value is a type of measurement that corresponds inversely to the amount of viral load in a given sample. Researchers have found that Ct values of 13-17 indicate high viral load, whereas Ct values greater than 34 indicate a lack of infectious virus.)
"We believe this should be an at-home test, but [if FDA approval comes through] the first rollout is to do this in laboratories, hospitals, and clinics."
"We believe that population screening devices have an immediate place and use in helping beat the virus," says Ferré. "You can have a significant impact even with a test at 60% sensitivity if you are testing frequently."
When presented with criticism of its recommendations, the FDA indicated that it will not automatically deny any at-home test that fails to meet the 90 percent sensitivity guidance.
"FDA is always open to alternative proposals from developers, including strategies for serial testing with less sensitive tests," a spokesperson wrote in a statement. "For example, it is possible that overall sensitivity of the strategy could be considered cumulatively rather than based on one-time testing….In the case of a manufacturer with an at-home test that can only detect people with COVID-19 when they have a high viral load, we encourage them to talk with us so we can better understand their test, how they propose to use it, and the validation data they have collected to support that use."
However, the FDA's actions so far conflict with its stated openness. e25 ended up adding a step to the protocol in order to better meet FDA standards for sensitivity, but that extra step—sending samples to a laboratory for results—will undercut the test's ability to work as an at-home screening tool.
"We believe this should be an at-home test, but [if FDA approval comes through] the first rollout is to do this in laboratories, hospitals, and clinics," Ferré says.
According to the FDA, no test developers have approached them with a request for an emergency use authorization that proposes an alternate testing paradigm, such as serial testing, to mitigate test sensitivity below 80 percent.
From a scientific perspective, antigen tests like e25Bio's are not the only horse in the race for a simple rapid test with potential for at-home use. CRISPR technology has long been touted as fertile ground for diagnostics, and in an eerily prescient interview with LeapsMag in November, CRISPR pioneer Feng Zhang spoke of its potential application as an at-home diagnostic for an infectious disease specifically.
"I think in the long run it will be great to see this for, say, at-home disease testing, for influenza and other sorts of important public health [concerns]," he said in the fall. "To be able to get a readout at home, people can potentially quarantine themselves rather than traveling to a hospital and then carrying the risk of spreading that disease to other people as they get to the clinic."
Zhang's company Sherlock Biosciences is now working on scaled-up manufacturing of a test to detect SARS CoV-2. Mammoth Biosciences, which secured funding from the National Institutes of Health's Rapid Acceleration of Diagnostics program, is also working on a CRISPR diagnostic for SARS CoV-2. Both would check the box for rapid testing, but so far not for at-home testing, as they would also require laboratory infrastructure to provide results.
If any at-home tests can clear the regulatory hurdles, they would also need to be manufactured on a large scale and be cheap enough to entice people to actually use them. In the world of at-home diagnostics, pregnancy tests have become the sole mainstream victor because they're simple to use, small to carry, easy to interpret, and costs about seven or eight dollars at any ubiquitous store, like Target or Walmart. By comparison, the at-home COVID collection tests that don't even offer diagnostics—you send away your sample to an external lab—all cost over $100 to take just one time.
For the time being, the only available diagnostics for COVID require a lab or an expensive dedicated machine to process. This disconnect could prolong the world's worst health crisis in a century.
"Daily rapid tests have enormous potential to sever transmission chains and create herd effects similar to herd immunity," Mina says. "We all recognize that vaccines and infections can result in herd immunity when something around half of people are no longer susceptible.
"The same thing exists with these tests. These are the intervention to stop the virus. If half of people choose to use these tests every other day, then we can stop transmission faster than a vaccine can. The technology exists, the theory and mathematics back it up, the epidemiology is sound. There is no reason we are not approaching this as strongly as we would be approaching vaccines."
--Additional reporting by Julia Sklar
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.
Coronavirus Risk Calculators: What You Need to Know
People in my family seem to develop every ailment in the world, including feline distemper and Dutch elm disease, so I naturally put fingers to keyboard when I discovered that COVID-19 risk calculators now exist.
"It's best to look at your risk band. This will give you a more useful insight into your personal risk."
But the results – based on my answers to questions -- are bewildering.
A British risk calculator developed by the Nexoid software company declared I have a 5 percent, or 1 in 20, chance of developing COVID-19 and less than 1 percent risk of dying if I get it. Um, great, I think? Meanwhile, 19 and Me, a risk calculator created by data scientists, says my risk of infection is 0.01 percent per week, or 1 in 10,000, and it gave me a risk score of 44 out of 100.
Confused? Join the club. But it's actually possible to interpret numbers like these and put them to use. Here are five tips about using coronavirus risk calculators:
1. Make Sure the Calculator Is Designed For You
Not every COVID-19 risk calculator is designed to be used by the general public. Cleveland Clinic's risk calculator, for example, is only a tool for medical professionals, not sick people or the "worried well," said Dr. Lara Jehi, Cleveland Clinic's chief research information officer.
Unfortunately, the risk calculator's web page fails to explicitly identify its target audience. But there are hints that it's not for lay people such as its references to "platelets" and "chlorides."
The 19 and Me or the Nexoid risk calculators, in contrast, are both designed for use by everyone, as is a risk calculator developed by Emory University.
2. Take a Look at the Calculator's Privacy Policy
COVID-19 risk calculators ask for a lot of personal information. The Nexoid calculator, for example, wanted to know my age, weight, drug and alcohol history, pre-existing conditions, blood type and more. It even asked me about the prescription drugs I take.
It's wise to check the privacy policy and be cautious about providing an email address or other personal information. Nexoid's policy says it provides the information it gathers to researchers but it doesn't release IP addresses, which can reveal your location in certain circumstances.
John-Arne Skolbekken, a professor and risk specialist at Norwegian University of Science and Technology, entered his own data in the Nexoid calculator after being contacted by LeapsMag for comment. He noted that the calculator, among other things, asks for information about use of recreational drugs that could be illegal in some places. "I have given away some of my personal data to a company that I can hope will not misuse them," he said. "Let's hope they are trustworthy."
The 19 and Me calculator, by contrast, doesn't gather any data from users, said Cindy Hu, data scientist at Mathematica, which created it. "As soon as the window is closed, that data is gone and not captured."
The Emory University risk calculator, meanwhile, has a long privacy policy that states "the information we collect during your assessment will not be correlated with contact information if you provide it." However, it says personal information can be shared with third parties.
3. Keep an Eye on Time Horizons
Let's say a risk calculator says you have a 1 percent risk of infection. That's fairly low if we're talking about this year as a whole, but it's quite worrisome if the risk percentage refers to today and jumps by 1 percent each day going forward. That's why it's helpful to know exactly what the numbers mean in terms of time.
Unfortunately, this information isn't always readily available. You may have to dig around for it or contact a risk calculator's developers for more information. The 19 and Me calculator's risk percentages refer to this current week based on your behavior this week, Hu said. The Nexoid calculator, by contrast, has an "infinite timeline" that assumes no vaccine is developed, said Jonathon Grantham, the company's managing director. But your results will vary over time since the calculator's developers adjust it to reflect new data.
When you use a risk calculator, focus on this question: "How does your risk compare to the risk of an 'average' person?"
4. Focus on the Big Picture
The Nexoid calculator gave me numbers of 5 percent (getting COVID-19) and 99.309 percent (surviving it). It even provided betting odds for gambling types: The odds are in favor of me not getting infected (19-to-1) and not dying if I get infected (144-to-1).
However, Grantham told me that these numbers "are not the whole story." Instead, he said, "it's best to look at your risk band. This will give you a more useful insight into your personal risk." Risk bands refer to a segmentation of people into five categories, from lowest to highest risk, according to how a person's result sits relative to the whole dataset.
The Nexoid calculator says I'm in the "lowest risk band" for getting COVID-19, and a "high risk band" for dying of it if I get it. That suggests I'd better stay in the lowest-risk category because my pre-existing risk factors could spell trouble for my survival if I get infected.
Michael J. Pencina, a professor and biostatistician at Duke University School of Medicine, agreed that focusing on your general risk level is better than focusing on numbers. When you use a risk calculator, he said, focus on this question: "How does your risk compare to the risk of an 'average' person?"
The 19 and Me calculator, meanwhile, put my risk at 44 out of 100. Hu said that a score of 50 represents the typical person's risk of developing serious consequences from another disease – the flu.
5. Remember to Take Action
Hu, who helped develop the 19 and Me risk calculator, said it's best to use it to "understand the relative impact of different behaviors." As she noted, the calculator is designed to allow users to plug in different answers about their behavior and immediately see how their risk levels change.
This information can help us figure out if we should change the way we approach the world by, say, washing our hands more or avoiding more personal encounters.
"Estimation of risk is only one part of prevention," Pencina said. "The other is risk factors and our ability to reduce them." In other words, odds, percentages and risk bands can be revealing, but it's what we do to change them that matters.