7 Things to Know about the U.S.’s Capability to Detect Omicron
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
A visualization of the original coronavirus causing COVID-19, which has now been detected across the globe in a highly mutated form called Omicron.
If the new variant Omicron isn’t here already – which many experts suspect that it is – it will be soon. While we wait for scientists to conduct the necessary research to characterize its transmissibility, potential fitness at immune evasion, and disease severity, we wanted to give Leaps.org readers a window into how the U.S. is positioned to detect the variant. So we spoke to Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories, a membership organization that represents state and local government health labs in the United States. Here are seven insights she shared.
1) If you test positive for COVID-19 with a standard PCR test, the diagnostic report will not tell you which variant you have. There are no diagnostic tests available for your doctor to order to identify variants. To find out the variant, the specimen must be sent to a commercial, clinical, academic, or public health laboratory for genetic sequencing.
2) Today, the U.S. sequences about 5 to 10 percent of all diagnostic specimens that test positive for SARS-CoV-2 in order to determine which variants are circulating and where. Last week nationally, for example, labs sequenced about 80,000 samples. This represents a massive increase from last year at this time, when labs were only sequencing about 8,000 specimens per week. Currently, 99.5 percent of circulating SARS-CoV-2 virus in the U.S. is the Delta variant.
3) The U.S. is “very well prepared” to detect Omicron, Wroblewski says, “particularly compared to where we were when the Alpha variant, or B117 first emerged.” Of the hunt for Omicron, she adds, “it’s very reminiscent of that time, except we are doing so much more sequencing and we have so much better coverage with our sequencing geographically, and we're doing it in a much more timely way. We have the ability to find emerging variants that are circulating in 0.01 percent of the population.”
4) Deciding which specimens to sample is not totally random. Samples that have more virus are likely to lead to better sequencing results. Labs also look to have a diverse set of representative samples, meaning across geographic regions and across gender, race, ethnicity, and age groups. Clinical diversity is also important, such as including pregnant women, severe in-patient cases, mild cases, etc.
5) Sequencing more is not necessarily better to find Omicron faster. “We will increase the number of sequences to a certain extent,” Wroblewski says. “Where we exhibit some caution is doing that indiscriminately isn’t the most effective use of time and resources. The important thing is to try to find Omicron, and if you increase your testing capacity too much, right now, it's still predominantly Delta in the U.S. by a long shot. So you’re mostly going to sequence Delta and you run the risk of delaying your discovery of Omicron, if you focus solely on increasing sequencing.”
So besides just ramping up the sheer numbers of sequencing, diagnostic labs across the country are now advised to preferentially use a certain PCR test made by Thermo Fisher that can help hasten the detection of Omicron. It turns out that Omicron’s specific mutations in the Spike protein mean that the Spike is not picked up on this PCR test, which yields a type of result called an S-gene target failure. Yet the test will still accurately pick up a COVID-19 diagnosis, because it detects two other gene targets on Omicron that are not mutated. “That S-gene target failure gives you a good indication that you may have Omicron. It’s a good early screen.”
Labs will then still need to sequence the whole genome to confirm it matches the Omicron sequence. “So right now, the new recommendation is to use [the Thermo Fisher test] as much as possible to give us a better chance of detecting Omicron more quickly.”
6) This Thermo Fisher test is “fairly widely used” in the U.S. already, so many labs are already well positioned to make the shift. “In early to mid 2020,” Wroblewski explains, “when the supply chain issue for testing was acute, many public health labs implemented five, six, seven, eight different tests, just so they could get enough supplies to do all the testing. Now that we're in a much better place supply-chain wise, it's very difficult and time consuming and cumbersome to maintain all those different test methods all the time, and many, many labs scaled back to only one or two. And so this [new recommendation] would just be shifting to two for some labs that will be shifting to them.”
7) Once Omicron is found here, labs will be focused on finding as many cases as possible, and the CDC will be conducting a variety of studies to determine the impact of the variant on diagnostics, therapeutics, and vaccines. Epidemiologists at the local, state, and federal level will analyze which populations it is spreading in, as well as the severity of the disease it causes. They will work to sort out different impacts on vaccinated vs. unvaccinated populations. The ultimate goal, Wroblewski concludes, is to “use all of that information to make better public health decisions and inform the public about what’s going on.”
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.
Urinary tract infections account for more than 8 million trips to the doctor each year.
Few things are more painful than a urinary tract infection (UTI). Common in men and women, these infections account for more than 8 million trips to the doctor each year and can cause an array of uncomfortable symptoms, from a burning feeling during urination to fever, vomiting, and chills. For an unlucky few, UTIs can be chronic—meaning that, despite treatment, they just keep coming back.
But new research, presented at the European Association of Urology (EAU) Congress in Paris this week, brings some hope to people who suffer from UTIs.
Clinicians from the Royal Berkshire Hospital presented the results of a long-term, nine-year clinical trial where 89 men and women who suffered from recurrent UTIs were given an oral vaccine called MV140, designed to prevent the infections. Every day for three months, the participants were given two sprays of the vaccine (flavored to taste like pineapple) and then followed over the course of nine years. Clinicians analyzed medical records and asked the study participants about symptoms to check whether any experienced UTIs or had any adverse reactions from taking the vaccine.
The results showed that across nine years, 48 of the participants (about 54%) remained completely infection-free. On average, the study participants remained infection free for 54.7 months—four and a half years.
“While we need to be pragmatic, this vaccine is a potential breakthrough in preventing UTIs and could offer a safe and effective alternative to conventional treatments,” said Gernot Bonita, Professor of Urology at the Alta Bro Medical Centre for Urology in Switzerland, who is also the EAU Chairman of Guidelines on Urological Infections.
The news comes as a relief not only for people who suffer chronic UTIs, but also to doctors who have seen an uptick in antibiotic-resistant UTIs in the past several years. Because UTIs usually require antibiotics, patients run the risk of developing a resistance to the antibiotics, making infections more difficult to treat. A preventative vaccine could mean less infections, less antibiotics, and less drug resistance overall.
“Many of our participants told us that having the vaccine restored their quality of life,” said Dr. Bob Yang, Consultant Urologist at the Royal Berkshire NHS Foundation Trust, who helped lead the research. “While we’re yet to look at the effect of this vaccine in different patient groups, this follow-up data suggests it could be a game-changer for UTI prevention if it’s offered widely, reducing the need for antibiotic treatments.”
MILESTONE: Doctors have transplanted a pig organ into a human for the first time in history
A surgeon at Massachusetts General Hospital prepares a pig organ for transplant.
Surgeons at Massachusetts General Hospital made history last week when they successfully transplanted a pig kidney into a human patient for the first time ever.
The recipient was a 62-year-old man named Richard Slayman who had been living with end-stage kidney disease caused by diabetes. While Slayman had received a kidney transplant in 2018 from a human donor, his diabetes ultimately caused the kidney to fail less than five years after the transplant. Slayman had undergone dialysis ever since—a procedure that uses an artificial kidney to remove waste products from a person’s blood when the kidneys are unable to—but the dialysis frequently caused blood clots and other complications that landed him in the hospital multiple times.
As a last resort, Slayman’s kidney specialist suggested a transplant using a pig kidney provided by eGenesis, a pharmaceutical company based in Cambridge, Mass. The highly experimental surgery was made possible with the Food and Drug Administration’s “compassionate use” initiative, which allows patients with life-threatening medical conditions access to experimental treatments.
The new frontier of organ donation
Like Slayman, more than 100,000 people are currently on the national organ transplant waiting list, and roughly 17 people die every day waiting for an available organ. To make up for the shortage of human organs, scientists have been experimenting for the past several decades with using organs from animals such as pigs—a new field of medicine known as xenotransplantation. But putting an animal organ into a human body is much more complicated than it might appear, experts say.
“The human immune system reacts incredibly violently to a pig organ, much more so than a human organ,” said Dr. Joren Madsen, director of the Mass General Transplant Center. Even with immunosuppressant drugs that suppress the body’s ability to reject the transplant organ, Madsen said, a human body would reject an animal organ “within minutes.”
So scientists have had to use gene-editing technology to change the animal organs so that they would work inside a human body. The pig kidney in Slayman’s surgery, for instance, had been genetically altered using CRISPR-Cas9 technology to remove harmful pig genes and add human ones. The kidney was also edited to remove pig viruses that could potentially infect a human after transplant.
With CRISPR technology, scientists have been able to prove that interspecies organ transplants are not only possible, but may be able to successfully work long term, too. In the past several years, scientists were able to transplant a pig kidney into a monkey and have the monkey survive for more than two years. More recently, doctors have transplanted pig hearts into human beings—though each recipient of a pig heart only managed to live a couple of months after the transplant. In one of the patients, researchers noted evidence of a pig virus in the man’s heart that had not been identified before the surgery and could be a possible explanation for his heart failure.
So far, so good
Slayman and his medical team ultimately decided to pursue the surgery—and the risk paid off. When the pig organ started producing urine at the end of the four-hour surgery, the entire operating room erupted in applause.
Slayman is currently receiving an infusion of immunosuppressant drugs to prevent the kidney from being rejected, while his doctors monitor the kidney’s function with frequent ultrasounds. Slayman is reported to be “recovering well” at Massachusetts General Hospital and is expected to be discharged within the next several days.