CDC Coding Error Led To Overcount of 72,000 COVID-19 Deaths

Last week, after reporting from the Guardian on mortality rates among children, the CDC corrected a “coding logic error” that had inadvertently added more than 72,000 Covid deaths of all ages to the data tracker, one of the most publicly accessible sources for Covid data. The Guardian reports: The agency briefly noted the change in a footnote, although the note did not explain how the error occurred or how long it was in effect. A total of 72,277 deaths in all age groups reported across 26 states were removed from the tracker “because CDC’s algorithm was accidentally counting deaths that were not Covid-19-related,” Jasmine Reed, a spokesperson for the agency, told the Guardian. The problem stemmed from two questions the CDC asks of states and jurisdictions when they report fatalities, according to a source familiar with the issue.

One data field asks if a person died “from illness/complications of illness,” and the field next to this asks for the date of death. When the answer is yes, then the date of death should be provided. But a problem apparently arose if a respondent included the date of death in this field even when the answer was “no” or “unknown.” The CDC’s system assumed that if a date was provided, then the “no” or “unknown” answer was an error, and the system switched the answer to “yes.” This resulted in an overcount of deaths due to Covid in the demographic breakdown, and the error, once discovered, was corrected last week. The CDC did not answer a question on how long the coding error was in effect.

“Working with near real-time data in an emergency is critical to guide decision-making, but may also mean we often have incomplete information when data are first reported,” said Reed. The death counts in the data tracker are “real-time and subject to change,” Reed noted, while numbers from the National Center for Health Statistics, a center within the CDC, are “the most complete source of death data,” despite lags in reporting, because the process includes a review of death certificates.

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Scientists Say They Can Read Nearly the Whole Genome of an IVF-Created Embryo

sciencehabit shares a report from Science.org: A California company says it can decipher almost all the DNA code of a days-old embryo created through in vitro fertilization (IVF) — a challenging feat because of the tiny volume of genetic material available for analysis. The advance depends on fully sequencing both parents’ DNA and “reconstructing” an embryo’s genome with the help of those data. And the company suggests it could make it possible to forecast risk for common diseases that develop decades down the line. Currently, such genetic risk prediction is being tested in adults, and sometimes offered clinically. The idea of applying it to IVF embryos has generated intense scientific and ethical controversy. But that hasn’t stopped the technology from galloping ahead.
Predicting a person’s chance of a specific illness by blending this genetic variability into what’s called a “polygenic risk score” remains under study in adults, in part because our understanding of how gene variants come together to drive or protect against disease remains a work in progress. In embryos it’s even harder to prove a risk score’s accuracy, researchers say. The new work on polygenic risk scores for IVF embryos is “exploratory research,” says Premal Shah, CEO of MyOme, the company reporting the results. Today in Nature Medicine, the MyOme team, led by company co-founders and scientists Matthew Rabinowitz and Akash Kumar, along with colleagues elsewhere, describe creating such scores by first sequencing the genomes of 10 pairs of parents who had already undergone IVF and had babies. The researchers then used data collected during the IVF process: The couples’ embryos, 110 in all, had undergone limited genetic testing at that time, a sort of spot sequencing of cells, called microarray measurements. Such analysis can test for an abnormal number of chromosomes, certain genetic diseases, and rearrangements of large chunks of DNA, and it has become an increasingly common part of IVF treatment in the United States. By combining these patchy embryo data with the more complete parental genome sequences, and applying statistical and population genomics techniques, the researchers could account for the gene shuffling that occurs during reproduction and calculate which chromosomes each parent had passed down to each embryo. In this way, they could predict much of that embryo’s DNA.

The researchers had a handy way to see whether their reconstruction was accurate: Check the couples’ babies. They collected cheek swab samples from the babies and sequenced their full genome, just as they’d done with the parents. They then compared that “true sequence” with the reconstructed genome for the embryo from which the child originated. The comparison revealed, essentially, a match: For a 3-day-old embryo, at least 96% of the reconstructed genome aligned with the inherited gene variants in the corresponding baby; for a 5-day-old embryo, it was at least 98%. (Because much of the human genome is the same across all people, the researchers focused on the DNA variability that made the parents, and their babies, unique.) Once they had reconstructed embryo genomes in hand, the researchers turned to published data from large genomic studies of adults with or without common chronic diseases and the polygenic risk score models that were derived from that information. Then, MyOme applied those models to the embryos, crunching polygenic risk scores for 12 diseases, including breast cancer, coronary artery disease, and type 2 diabetes. The team also experimented with combining the reconstructed embryo sequence of single genes, such as BRCA1 and BRCA2, that are known to dramatically raise risk of certain diseases, with an embryo’s polygenic risk scores for that condition — in this case, breast cancer.

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This Year’s Flu Vaccine Was Basically Worthless

This winter’s flu vaccine was a particularly bad match for the most common influenza strain in circulation, a new analysis from the Centers for Disease Control and Prevention found. Gizmodo reports: Thankfully, the flu season was much milder than usual for the second year in a row, as ongoing covid-19 precautions likely blunted the spread of flu as well. The estimates come from the CDC’s long-running surveillance program of people with suspected flu-like symptoms who visit various outpatient sites throughout the country. Overall, the odds of catching a case of confirmed flu were only slightly lower for vaccinated people, the researchers found. Against all flu strains detected at these sites, the vaccine was deemed to be 14% effective, as well as 16% effective at preventing cases of flu from A(H3N2) viruses, the predominant strain this winter. Numbers this low are far below the 50% threshold for a vaccine to be considered relatively useful, and they’re not even high enough to reach statistical significance.

In the words of the researchers, who published their results in the CDC’s Morbidity and Mortality Weekly Report, the vaccine “did not reduce the risk for outpatient respiratory illness caused by influenza A(H3N2) viruses that have predominated so far this season.” Flu vaccines, even in a good year, are far from perfect. The strains of influenza virus that infect humans are constantly evolving, meaning that scientists have to try to predict what these strains will look like during the next flu season so that they can match them to the strains included in the vaccine (the vaccine will usually include four strains at a time). This guessing game often results in a vaccine that’s around 50% to 60% effective, but sometimes, as is the case this year, the mismatch can get worse. It doesn’t help that this year’s main flu is H3N2, a subtype of flu already known for being harder to predict than others.

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Next-Generation Spinal Implants Help People With Severe Paralysis Walk, Cycle, and Swim

sciencehabit shares a report from Science.org: Three men paralyzed in motorcycle accidents have become the first success stories for a new spinal stimulation device that could enable faster and easier recoveries than its predecessors. The men, who had no sensation or control over their legs, were able to take supported steps within 1 day of turning on the electrical stimulation, and could stroll outside with a walker after a few months, researchers report today. The nerve-stimulating device doesn’t cure spinal cord injury, and it likely won’t eliminate wheelchair use, but it raises hopes that the assistive technology is practical enough for widespread use.

For now, sending commands to the device is cumbersome. Users must select their desired movement on a tablet, which sends Bluetooth commands to a transmitter worn around the waist. That device must be positioned next to a ‘pulse generator’ implanted in the abdomen, which then activates electrodes along the spine. Setting up to use the stimulation takes 5 to 10 minutes. But the next generation of devices should allow users to activate the pulse generator by giving voice commands to a smartwatch. The company behind the technology plans to test this newer mobility system in a multisite clinical trial of 70 to 100 participants that the team hopes will lead to U.S. regulatory approval. The researchers reported their findings in the journal Nature Medicine.

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Can Mapping Differences in Cancer Rates Help Pinpoint Environmental Factors?

“Scientists have made the first steps to develop an atlas of world cancer, hoping it will bring us closer to a cure,” reports the Telegraph.

“A map showing stark differences in the incidence of 10 types of cancer between Spain and Portugal has sparked a race to pinpoint causes and risk factors people should avoid.”

It shows huge differences for people living only a short distance apart, sometimes across the border between Spain and Portugal, and others occurring within the same country. Scientists say it will take years to solve the puzzle completely but are confident that the map provides the pieces. There are easier questions and more complex riddles. But it all points to environmental factors — as opposed to genetics — playing a major role in causing cancers.

The lung cancer map tells a clear story of far higher levels of smoking tobacco in Spain than in Portugal, with the latter country showing a consistent hue of dark blue for a lower risk of mortality, while Spain has large areas lit up in red, at least on the map representing men. Twenty per cent of Spanish adults are daily smokers, compared with just over 11 per cent in Portugal. But the data from cancer of the larynx, also linked to smoking, tells a vastly different story, with a high mortality risk for men shown straddling the border in southern Portugal and south western Spain, as well as patches in the north of both countries. “The lung cancer and smoking connection is very clear, so why in other cancers that have a strong link with tobacco are we seeing such surprising differences?” asks Pablo Fernández-Navarro, the lead co-ordinator of the atlas from the Spanish side.

“This is what is so fantastic. If whole countries had uniform levels of mortality, the maps would be in plain colours. Given that it is not the case, now we have to investigate and explain these differences, eliminating one factor after another,” Fernández-Navarro told The Telegraph.

In the case of larynx cancer, the Spanish epidemiologist says the map confirms that smoking is by no means the only risk factor, and that other elements must also be at work, from alcohol intake to levels of pollutants such as asbestos or petrochemicals in the environment.

Thanks to Slashdot reader Bruce66423 for sharing the link.

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‘Pulsed Electromagnetic Energy’ Could Cause Havana Syndrome

An intelligence panel investigating the cause of a spate of mysterious incidents that have struck dozens of US officials across the globe has said that some of the episodes could “plausibly” have been caused by “pulsed electromagnetic energy” emitted by an external source, according to an executive summary of the panel’s findings released Wednesday. CNN reports: But the panel stopped short of making a definitive determination, saying only that both electromagnetic energy and, in limited circumstances, ultrasound could explain the key symptoms — highlighting the degree to which the murky illness known colloquially as “Havana Syndrome” has remained one of the intelligence community’s most stubborn mysteries. “We’ve learned a lot,” an intelligence official familiar with the panel’s work told reporters, speaking on anonymity under terms set by the Office of the Director of National Intelligence. “While we don’t have the specific mechanism for each case, what we do know is if you report quickly and promptly get medical care, most people are getting well.”

The scientific panel emphasized that the cases it studied were “genuine and compelling,” noting that some incidents have affected multiple people in the same space and clinical samples from a few victims have shown signs of “cellular injury to the nervous system.” An executive summary of the panel’s work provided new details about how the government is categorizing cases as possible Havana Syndrome, a clinically vague illness that has long frustrated firm diagnosis because victims have suffered from such a diverse array of symptoms. Although officials declined to say how many cases the panel examined as part of its inquiry, they said they studied cases that met four “core characteristics”: the acute onset of sounds or pressure, sometimes in only one ear or on one side of the head; simultaneous symptoms of vertigo, loss of balance and ear pain; “a strong sense of locality or directionality”; and the absence of any known environmental or medical conditions that could have caused the other symptoms.

Both pulsed electromagnetic energy, “particularly in the radiofrequency range,” and ultrasonic arrays could feasibly cause the four core symptoms, the panel found. Both could originate from “a concealable source.” But ultrasound can’t travel through walls, the panel found, “restricting its applicability to scenarios in which the source is near the target.”
Sources of radiofrequency energy, on the other hand, are known to exist, “could generate the required stimulus, are concealable, and have moderate power requirements,” the panel said. “Using nonstandard antennas and techniques, the signals could be propagated with low loss through air for tens to hundreds of meters, and with some loss, through most building materials.” But intelligence officials familiar with the panel’s work emphasized that important information gaps remained, forestalling them from reaching firmer conclusions. The experts panel also ruled out so-called psycho-social factors. They also ruled out “ionizing radiation, chemical and biological agents, infrasound, audible sound, ultrasound propagated over large distances, and bulk heating from electromagnetic energy.”

“The panel made seven recommendations, including developing better biomarkers that are ‘more specific and more sensitive for diagnosis and triage’ of cases,” reports CNN. “It also recommended utilizing ‘detectors’ and obtaining ‘devices to aid research.’ Finally, officials urged swift action by medical officials whenever a case is reported, emphasizing that individuals who have been treated immediately after an event have improved.”

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