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.
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.
How to have a good life, based on the world's longest study of happiness
What makes for a good life? Such a simple question, yet we don't have great answers. Most of us try to figure it out as we go along, and many end up feeling like they never got to the bottom of it.
Shouldn't something so important be approached with more scientific rigor? In 1938, Harvard researchers began a study to fill this gap. Since then, they’ve followed hundreds of people over the course of their lives, hoping to identify which factors are key to long-term satisfaction.
Eighty-five years later, the Harvard Study of Adult Development is still going. And today, its directors, the psychiatrists Bob Waldinger and Marc Shulz, have published a book that pulls together the study’s most important findings. It’s called The Good Life: Lessons from the World’s Longest Scientific Study of Happiness.
In this podcast episode, I talked with Dr. Waldinger about life lessons that we can mine from the Harvard study and his new book.
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More background on the study
Back in the 1930s, the research began with 724 people. Some were first-year Harvard students paying full tuition, others were freshmen who needed financial help, and the rest were 14-year-old boys from inner city Boston – white males only. Fortunately, the study team realized the error of their ways and expanded their sample to include the wives and daughters of the first participants. And Waldinger’s book focuses on the Harvard study findings that can be corroborated by evidence from additional research on the lives of people of different races and other minorities.
The study now includes over 1,300 relatives of the original participants, spanning three generations. Every two years, the participants have sent the researchers a filled-out questionnaire, reporting how their lives are going. At five-year intervals, the research team takes a peek their health records and, every 15 years, the psychologists meet their subjects in-person to check out their appearance and behavior.
But they don’t stop there. No, the researchers factor in multiple blood samples, DNA, images from body scans, and even the donated brains of 25 participants.
Robert Waldinger, director of the Harvard Study of Adult Development.
Katherine Taylor
Dr. Waldinger is Clinical Professor of Psychiatry at Harvard Medical School, in addition to being Director of the Harvard Study of Adult Development. He got his M.D. from Harvard Medical School and has published numerous scientific papers he’s a practicing psychiatrist and psychoanalyst, he teaches Harvard medical students, and since that is clearly not enough to keep him busy, he’s also a Zen priest.
His book is a must-read if you’re looking for scientific evidence on how to design your life for more satisfaction so someday in the future you can look back on it without regret, and this episode was an amazing conversation in which Dr. Waldinger breaks down many of the cliches about the good life, making his advice real and tangible. We also get into what he calls “side-by-side” relationships, personality traits for the good life, and the downsides of being too strict about work-life balance.
Show links
- Bob Waldinger
- Waldinger's book, The Good Life: Lessons from the World's Longest Scientific Study of Happiness
- The Harvard Study of Adult Development
- Waldinger's Ted Talk
- Gallup report finding that people with good friends at work have higher engagement with their jobs
- The link between relationships and well-being
- Those with social connections live longer
The Friday Five: A new blood test to detect Alzheimer's
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
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Here are the promising studies covered in this week's Friday Five:
- A blood test to detect Alzheimer's
- War vets can take their psychologist wherever they go
- Does intermittent fasting affect circadian rhythms?
- A new year's resolution for living longer
- 3-D printed eyes?